The problem is both Matt and Peter can't read minds. They read thoughts that people are thinking at that point. Neither one has shown the ability to read anything else. That's why Matt couldn't find out anything from Angela Petrelli because she was screaming at him to get out, and he couldn't get anything from Bennett because he was thinking in Japanese.
So, if time is frozen, they have no active thoughts, therefore nothing for Peter to read.
hmm fair enough i guess, if he cant read minds and just thoughts it would need to either just talk to them casually, go invisible and thought read and then his miffed, and loses because if his objective is to clear his name, i cant see anything in this scenario that can help him. even if he did kill them all, that would add more on his blacklist of hates