I think you can accept a limited form of obedience to authority as part of your quest for a moral code. For example, someone decided that "red means stop and green means go". It was an arbitrary decision, but you can accept it is in your self-interest to follow it.
By extension, a division of labor produces a hierarchy which is not inconsistent with a self-decided moral code--- you may like to design airplanes, and someone else might like to fly them. There is a hierarchy implicit in this--- the pilot is the only one who is allowed to fly the plane, the designer decides where the wings should go and how they should slant. This type of authority structure doesn't seem inconsistent with a personal ethical code.
The basic issue here is whether the division of labor is actually efficient, and for a free market model, this hinges on free-entry using wage as a signal--- the positions of airline pilot and airplane engineer are basically free entry, anyone can apply, and you can see that they are free because they are paid with a wage determined competitively. The educational and professional requirements are not particularly onerous, requiring only a certain amount of college for one, perhaps a Master's degree, and only a certain amount of flight experience for the other. Both can be acquired by a determined individual in a few years, and do not require climbing a hierarchy, or engaging in any self-denying fealty to a political order. So I think even Sartre accept this form of hierarchy and division of powers.
I believe the answer to your question is that an individualist can tolerate a heirarchy only when it is of this sort, when it is an expression of an efficient division of labor and knowledge. Realistically, in a market model, this happens only when it has free entry to all positions, based on competition and lowest-competent-bid. In this case one is not a hypocrit in obeying the decisions of the authority structure, because if one finds it incredibly onerous, one can enter this authority structure oneself with a reasonable amount of effort and a certain sacrifice of wage and time. This type of free-entry hierarchy can be consistent with an ethical code which comes from personal construction, and not from an exterior imposition, because one an accept those collective decisions which one has the power to influence without undue barrier. In such a system, the desire of people to be on top would make top positions extremely low-paid. There are plenty of highly competent people who would jump at the chance to be CEO of GM even for a salary of $20,000. On the other hand, they might forgo this decision making power and become a factory laborer, if the job paid $60,000. If you have a truly special skill, like programming embedded systems, you might get a very specialized niche job with a very high pay, like $100,000. This is what a competitive market equilibrium looks like, and it is consistent with an individual accepting the decisions of others, as a form of fair division of labor.
But the heirarchies which we find around us are not of this sort. They are externally constructed, and each powerful position comes with a social mechanism to produce artificial scarcity for the people who can fill it. This means that it doesn't require sacrifice to enter the top positions, far from it. High-corporate positions, start-up sucesses, political positions, leadership roles in religious institutions. These activities are not open to all, and are both highly sought and highly rewarded. This should never happen--- highly sought professions, like airline pilot, are supposed to be of low pay through the large number of people who seek them. If you think that there is a scarcity of people with such skills, consider that airline pilots, computer programmers, actuaries, each require a different extremely demanding skill set, but their salary has been driven to market average or below through competition. When you have a highly sought and highly paid position, you can be sure it is closed to all but a certain class of people, and that this closing off has nothing to do with skills, but with politics.
In each of these cases, it is easy to see the political forces. I have never seen a request for resumes to fill the job of CEO of GM. When you fill this position, you hire from the top administrators internally or from other CEO's, and the competition goes the other way--- the company competes as to how much they can afford to pay their CEO! Nobody has ever come up to a random devout Catholic, an individual priest or nun, and asked if she would like to be the Pope this year (although the Dalai Lama is selected by something close to this process). In start-up firms, the investors are looking for a guarantee of monopoly advantage, not for competitive return on capital. Try to run for political office without a party.
All these hierarchies are politically closed off to the individualist in a modern society. Such heirarchies conflict with the notion of individual freedom of conscience.
The natural state of human organization is to do stuff like this, one tier selects the next, and so on to the top. Actually, this is not quite true, there is also the more direct thing, where a guy grabs some guns and kills a bunch of people to establish authority, but let's assume we're past that. The process of producing tiered hierarchies will produce closed decision making segments of society, and then I think it is impossible for the individualist to obey the dictates of these closed organizations without hypocracy. No individual has any say in these decisions, since to get to this point, one must bow down to the established gods there.
But the solution cannot be anarchy, because anarchy doesn't diminish the power of closed political organizations. The notions of individualism only exists in societies which have both a strong religious tradition to free themselves from natural law (can't beat your slaves, no human experimentation, no torturous punishment) and even stronger secular government traditions that free them from religious law (no imposition of religion, freedom of conscience, freedom of speech). Without these guarantees, individualism is a hopeless fantasy--- you're either killed by the chief or burned at the stake.
Further, without some form of decentralized decision making, a way to allow new ventures, and to tolerate a certain amount of failure, you are also preventing individualism. If you are not protected from confiscation of property, your political opponents can squash your venture through legal action. So there is a tie in with modern economic structures too.
I think your only bet for maximizing individual development, and therefore maximizing the potential of innovation in a society, is to push for a form of government which is actively interested in atomizing collective power to as large a degree as possible. Such a state can't be anarchic--- it needs to enforce criminal law, to prevent chieftains from taking over. It needs to tax organizations progressively based on size, so as to break them up into manageable chunks that an individual can enter and affect without the corrosive anti-individualist selection involved in rising through endless ranks. It needs to demand competitive open-market hiring for all positions, as much as is feasible and compatible with individual freedom of association. It needs mechanisms to dilute great concentration of wealth, to prevent monopolization of decision making power, and it needs to battle information hoarding by public dissemination of ideas free of copyrights. The best you can expect in this direction is probably a progressive income tax and occasional half-hearted anti-trust action.
