Nah, I don't think so. Fuji won't be punished just because he's apologising for all those troubles, especially since WG's own shichibukai did a number on such a once peaceful country, even Gorosei couldn't deny it, I bet. They might blame Luffy + Law pirate alliance for wrecking the place up, but Doffy's deed was a big crime on their part.
I don't think Fuji would turn to RA, because it seems he rather changes the current Marine from the inside and he's still not accepting all pirates despite of his consideration to Luffy. Besides, looks like his goal is to demolish the shichibukai system, so he can't do that in easier way if he were to join RA. It's a bit different than how Aokiji takes care of things, where he believes there's other way to change the entire matter other than being a Marine.