I find it really stupid that one gets fined/bountied for friendly fire without any warning, specially while defending an installation. Come on, guys, I'm trying to save your skins here. Give me at least three strikes, may be?
Anyway, pay your bounty at Bacon Port through Interstellar Factors, NOT by turning yourself in at the Authority Contact, which will send you to jail, yes.
Also, for some reason your wanted status clears off upon coming out of SC at Bacon Port. You don't even get the anonymous access notice. Not sure if it's a bug or if it's by design while the CG lasts, but it's been happening to me all day. So you can safely request docking and land without risking getting blown up.