For God's sake, Flynn misled the Vice President of the United States, however important Flynn's job position might have been,m it's not as important as VP.
President Trump showed loyalty to his Vice President, and admirably so.
It would have been a slap in the face to let Flynn get away with such deceit, even though there was no underlying crime.
So that situation is apples and oranges compared to this one...
Pence is a close pal with Ryan and by extension Priebus.
Apparently Flynn just referenced their being able to talk about the issues he was bringing up after the inauguration. That’s arguably not “discussing” sanctions at all.
Pence was clearly a jerk about it—if he felt Flynn’s communication was incomplete, he could make sure that he wanted more detail in the future. Looking to have Flynn removed as he did was a clear shot at Trump.