I think it unlikely, but possible, that Flynn didn't talk to the Russians about sanctions and lied to Pence about something else. I also think it is unlikely, but possible that Pence knew exactly what Flynn was doing.
I agree with the second possibility and actually believe it is a real possibility.
However, regarding the first possibility, why would the Trump White House want to bring the Russia scandal back to the forefront if Flynn was fired for something else? The only reason I could imagine for that would be what Flynn was fired for was something a lot worse than the Russia scandal.