How do you tell the good inmates apart from the bad inmates?

A fair bit of the side-quests I've started in Batman: Arkham City are given by political prisoners usually by themselves on some roof. However, some thugs also like to sit by themselves on a roof, so more than once I've just walked up to them like they're someone nice then had to beat them down.

The run-of-the-mill inmate shows up as blue on Detective Vision, just like the political prisoners, so I don't see any easy way to tell them apart. Their posture seems to vary as well, but both can slouch, etc.

Is this not really a problem as you continue on (they're so rare)? Or rather, should I just assume everyone's bad and sneak up on them like a real Batman?

When a political prisoner appear, they usually will be being robbed by some thug. You can tell the difference by just watching who is afraid and who is not.

So it's fair to assume that everyone is bad until proven contrary.

Political prisoners ("good inmates") wear parkas. No one else does.