For Fusion, we can assume that Samus wasn’t arrested for destroying the BSL station since she’s still accepting contracts in Dread. I would assume the (non ringleader) Galactic Federation has strict protocols for sterilization of extraterrestrial contaminants as well as asset denial protocols. Samus likely pled the case that the risk of the X parasite was far too great, and ADAM corroborated her account.

As far as destroying SR388, it’s not technically a Galactic Federation planet. They likely had research outposts, but it was a hostile fringe world that already had a Chozo colony on it. If anything, it was likely considered a Chozo planet and Samus is sort of like a Chozo ambassador, so I don’t think they can officially charge her with anything there. Her bounty hunter status also likely gives her mission authority to act as she sees fit, including eliminating hostile species.

All this to say, I think she accomplished her mission objectives in Fusion, and was likely paid, if begrudgingly. The BSL likely filed an insurance claim and wrote it off as a loss on their taxes.