The main protagonist is John Hawkwood. English mercenary, lead a band of mercenaries known as the White Company. They went where the money was, occasionally hopping allegiances when the gold was good. Hawkwood in particular is often lauded as a hero to Florence, though there are critics of the title. The main antagonist is Pope Urban V. Pope, in a story where we assume that God exists, already in a position of moral goodness. Excommunicates all the free mercenaries for occasionally betraying the Church, wreaking havoc in the countryside, etc., etc. The two main conceits of this: one, not every free mercenary was deserving of excommunication (but in his position, I don't present him as wrong to do so - it was either that or let them cause chaos), and two, excommunicating somebody from the Church turns them into a werewolf.
During the story, Pope Urban V is basically trying to keep Europe together, recommunicating (is that the word?) many of those who he's excommunicated, doing his Papal duties, really nothing morally wrong. He's doing God's work and at no point is he ever placed as morally in the wrong for doing so. I suppose, in the grand scheme of things, you could argue that he's a gray character, since - you know - he's a Pope. Pre-Renaissance Catholic Church wasn't fantastic in any regard, and there were a couple of crusades going on in Urban V's reign. But as far as his role as a character in this story is concerned, he's a good guy. At worst, a servant of God with a lack of foresight.
John Hawkwood, meanwhile, is presented as one of the "better" free companies. The historical accuracy of that one is... lenient, but again, as a character in the story, he's not plundering between battles, mostly because he's got one of the finest free companies out there, so they rarely need the money. His perspective is that Pope Urban V basically let loose a bunch of werewolves on the European countryside, and I'm thinking perhaps giving him a tragic death at the hands of his wolf side - his first wife, likely, since so little is known about her - that motivates him to seek revenge/justice. Again, I'm presenting him as morally good. At worst, a loveable rogue with a Jekyll and Hyde complex.
If either side is gray, it'd be Hawkwood. But I do my damnedest to make him seem like a good guy, and I think he's at least as good as your average fantasy protagonist seeking the same sort of justice.