Is Harry just confused by his intuitions about the evil of slavery, without sufficient reflection?

That's certainly canon!Hermione's problem.

But there is something wrong with House-Elves, at least in canon, even after whatever went into their creation. They enjoy serving humans, fine; I'm with MoR!Harry about that. But (possibly unbeknownst to Harry and Hermione yet) there are House-Elves who are very unhappy with their current situation, such as Dobby (who disliked his master) and Winky (who loved her master but was fired and never recovered from this). It always bothered me that canon!Hermione never outgrew her early phase of S.P.E.W. and never tried to do anything that would actually help them. (However, the Word of God is that she did help them in her adulthood, so that's all right then.)