I think putting them in a position where their powers are useless, waiting for them to realize that fact, and just waiting until they don't use their powers long enough to let their personalities manifest, then interrogate them. It might be difficult to do this, especially since Epic powers seem to cause a sort of 'itch' in the Epic, which facing their fears negates.
I think that it should be noted that not all Epics were murderers like Newton, or criminals, like Steelheart. Some, like Regalia or Prof, were normal people. Killing them willy nilly, especially given an alternative, would be a bad idea.
There is also the possibility of getting a High Epic that is truly bad, having them face their fears, then having no weakness. Basically, you get an Epic that you can only kill via old age.