I don't think these telepaths were supposed to be sympathetic. That's how Lyta sees it, but not how the audience is supposed to take it. After all, and I believe this is revealed in the next few episodes or so so I'll put it in spoiler tags:
You don't get to that point by being a wholesome character.
However, Sheridan only sees telepaths as tools, and this was presented in the show in subtle ways. The way he uses the frozen telepaths for the civil war and how he regards their colony in Paragon of Animals: he wants them there so he can have telepaths on *his* side in the war and says as much to Garibaldi. It's not about them as people, it's about his strategy. Also, according to JMS this was the reason Sheridan saw himself in a Psi Corps uniform way back in the Kosh vision in season two - because he's treating the telepaths as Psi Corps does, as tools.