Several important facts need to be etablished.
If the Bonisagus took away items from a covenant he was banished from, the people coming to take it over can use appropriate sanctions and force to retrieve what is rightfully theirs. Hopw far they could go would be open to interpretation. Had they outright killed him, before asking him to surrender the items, that might have been a bit much. Or it might be ok, depending on lots of things.
One major point is how this troiupe and saga interprets hermetic justice. I've experienced some who play with the justice being quite fair and rational. And others who feel that the code is more of a guideline, and sure you might be charged, but political clout or pure force can get you out of it. I assume the system is mostly fair, but some political intrigue and pressure exists.
Depriving the Bonisagus of magic would IMHO only fly, if this wagon on fire actually destroyed or damaged something worthwile of his. A dead grog is a mundane resource. Actually, the Bonisagus is guilty if Depriving the newcomer magi, since they were to take over the covenant along with the library. If the library material he stole was damaged, there might even be a (further) case against him, because his crime and his refusal to surrender the stolen goods forced the PC magi into taking drastic measures, which in turn damaged the goods. A bit cheeky to do this, but a common legal tactic is to keep piling on accusations, as long as they are even mildly propable. Some of then ought to stick.
But a magus yelling "to hell with the code" does seem very unfortunate. If he doesn't want to obey the code, he can't be protected by it either. Forfeit immunity! Perhaps it was said in the heat of an argument, and he should get a second chance to decide whether he sticks to that opinion. But it was said before witnesses. And had he been a magus known to be dangerous with combat magic, saying this could IMHO easily justify a pre-emtive strike. Rather than wait for him to actually kill one of the nearby magi, before striking at him.
Vis fine for a mere inconvenience is too thin. I doubt any peripheral code rulings have fined someone this much vis for so little a problem. If it does exist, it would have been controversial back then. But it still might have happened. The future implications of this does suggest many squabbles over little matters, so I think a lot of magi would support ruling against this. And a lot of other magi, wanting this chaos, strife and easily exploitable situation, would support it. Not to mention any specific House, so as to not generalize and offend anyone. But Ixnay on the Ytalus-Tay.
But even if a Quaesitor rules this fine to be paid, the situation could and should be taken up at the following Tribunal.