Any chance that Flynn is a sleeper agent from a future Rittenhouse?
I doubt it very much.
However sympathetic his motives and goals, he's still a multiple murderer and temporal terrorist. He's crossed too many lines, and while I can accept the team working with him for the greater good, I really don't see him as suitable romance material for anyone.
Wyatt had went back in time to erase a guy from history because he wanted to resurrect Jessica. And he ended up killing someone. Even Lucy has killed an innocent in the name of maintaining her goal. Perhaps not as much as Flynn, but she has done it.