I think the Flynn thing was Flynn protecting Pence at a critical moment when Russia! Russia! Russia! looked like it could cause huge problems.
Pence had appeared on a Sunday Show and said that none of Team Trump had spoken to any Russian. Well Flynn had and Pence didn’t know about it.
Flynn could have defended himself but it would have fed the Russia!!! fire at the very beginning of the Trump admin and made it look like they were hiding contacts with Russia. So he let it look like he had lied to Pence and he took one for the team. JMO
I think you're right. From all I've seen, Flynn still seems to me to be an honorable man.