Yea, they were wrong, but in the scope of the writing, they were still supposed to be the wisest good guys whos only real flaw was their penchant for pacifism until they had no other choice. Yes, that goes against the other writing where they commissioned the clone army, but that was also corrupted in secret by a turncoat Jedi.

They're supposed to be the good guys, full stop. That doesn't mean the movie writers were capable of fully exploring how wrong pacifism and their other flaws are. (I say movies because I haven't read any of the extended universe books where they might actually luck on to some good writing)