Flynn seemed somewhat out of character. I know I haven't finished ToV yet (Just finished Baction portion), but Flynn was much more a rule-monger in the game and probably wouldn't have been privy to covering up Galista's death like they did, and in fact would've been more for capturing him and putting him on trial despite them acting in self-defense.
Was also under the impression Yuri left the knights under more distasteful terms. Hell, I would've bought him opting to take the rap for killing Galista on that note, but aside from seemingly not wanting to serve under anyone else but his captain, it was all kinda meh. Guess it kinda explains his blastia and Repede, though.