Yes and no, in certain cases; although I do highly agree with the idea that a Pokémon obeys the orders of its trainer, and thus perhaps lacks the capability to distinguish good from evil as a human does, there could be a slight alteration...
Some Pokémon perhaps can have a nigh-human (or surpassing-human, a la Alakazam) intellegence; primarily I suppose we see this in the anime, with the few Pokémon that have the ability to talk. Those that do, in my opinion, have the chance at truely possessing human intellegence or something very similiar to it. Ergo, if one desires to use the anime (and fanfiction) as their basis for this arguement, then those few Pokémon might have more of a capability to distinguish good from evil and act upon them in a human manner.
Now then, for solely-game canon, I don't believe this exists at all-- we haven't seen any talking Pokémon in the games, have we (with the exclusion of the Sinnoh myths, one of which mentions a conversation between a human and Pokémon)? The manga I can't speak for, however-- I've never read any of them.