Well the Bar with no Name Incident solidfies the fact that Frank really gives no shit about the whole Super Villain thing. They're criminals and he deals the same thing he does to criminals.
Microchips death ties into that as well. Frank's world is VERY black and white most of the time. Micro had sold him out to gangsters. If we're talking the same thing (I assume you mean the MAx series) then Frank even gave Micro a chance to leave and not get killed.