There's a lot of context-shifting in his post. The soldier example is one, here is another;

The capitalist who argues for the triumphant-against-adversity, morally justified businessman working in a perfectly competitive environment, the religious believer who argues for a view of religion as a peaceful, purpose-giving institution, or the libertarian who argues for a minimal government concerned with other people’s welfare, are all arguing from “ideal scenarios.” Yes, it would be better for all concerned if these scenarios were paradigmatic, but they are not. In fact, these scenarios are very rare, and generally out-norm. You cannot use a scenario that is out-norm for a given system to argue for that system itself as being desirable! This can only achieve the opposite of the effect intended, which is to say “if there are so few good agents like those you mention, then the system must be pretty bad indeed.” --Francois Tremblay ("Why Hierarchies are Immoral" paragraph 15)

Note the shift in context from what a given system is supposed to do to what other systems actually do. That is, he shifts from a context of evaluating theoretical concepts to historical data, and criticizes the theoretical concept on the basis of historical data which is not even relevant to the concept itself. That the data invoked is used for support of a broad generalization (some employers are mean to their employees, therefore all employers are immoral; some parents abuse their position of authority and some families are dysfunctional, therefore the family as such is immoral, etc.) that goes entirely beyond the scope of what such information can possibly provide.

Further, his insinuation that the employer/employee relationship is inherently unjust (further elaborated in the comments section) reads more like a critique of the concept of a market economy and of commerce generally. The idea that the laborer, the seller, is entitled to an employer, the buyer, is to say that the buyer is obliged to keep the seller in business. If it holds good here it must everywhere and if we grant it we must also grant that the seller is entitled to a buyer, and that force is justified in ensuring it is so. In comment 5 he runs roughshod over the concept of private property itself like a drunken sleigh driver. Is the job site/workplace not someone's private property? Does it not then follow that the owner(s) have the right to exclude anyone they so choose? What if I 'fire' one grocery store for providing inadequate goods? I know the rule of thumb for bodegas is that their produce must be rotten, but dag nabbit, that ain't good enough for me!

Any true deconstruction of a hierarchy cannot take place from within it, but rather from the outside, both because such deconstruction would not be permitted to exist and because the ideology of a person in a hierarchy is implicitly or explicitly molded by the aims of that hierarchy. --"Why Hierarchies are Immoral" paragraph 16

Right alongside lucid analysis seems an almost Hegelian infiltration. Given the nature of not only the state, but of hierarchy itself, how is one to overcome it, but to be a Great Man selected by History itself to change things? Must, otherwise, a Nietzschean Homo Superior emerge who are/is beyond hierarchy to spell its inevitable historical doom?

If I were to broadly classify Mr. Tremblay's error, I would say it is this; in attempt to 'thicken' the dialectal approach to libertarian philosophy to its ultimate limit, he's taken it beyond its proper context; it becomes more than a critique/normative argument of politics and ends up washing rip tide over ontology, aesthetics, ethics, morality, sociology, organizational theory and...really anything it can get its blobular hands upon. In echoes of Frankenstein, Tremblay's Monster is sure to produce heartache, disaster and Boris Karloff pictures in its wake.

That or Jorge's right and he's an idiot, or just being sloppy...