I don't understand. Are they terrorists, or are they non-evil? If they are harming or killing innocent people to accomplish their ends, they're evil. Regardless of those ends.

I'll assume you mean that they are non-terrorist Revolutionaries. Well, a lot of revolutionaries eventually find out that the people they are overthrowing are doing at least as good a job as they themselves could. (usually succesful revolutionaries, after the fact, or imprisoned revolutionaries, reading the papers every day from their cells.)

So really I think you have three choices.
1. Bad choice. Tell them as DM, "ha ha".
2. Let them talk to people with different viewpoints. Present some sympathetic characters that disagree with them, and have those characters be right some of the time (and wrong other times).
3. Let them "win" and try to pass rules, and watch how their mistakes hurt more people than the oppressors' ever did. (But still have some positive effects).