I'm not going to be sucked into another thread about INS, madness lies down that path. It's not a particularly good movie even apart from the horrible "dilemma."
But to answer the thread, yes, Picard is a hypocrite. Apart from a few technicalities, the situations are very similar, and in fact, there's a greater justification for removing the Baku than the Federation colonists.
I think they were just hoping Trek fans had forgotten or hadn't seen "journey's end."