:( The problem is, I'd rather not have that as a plot device. Besides, Equestria is never going to annex the Elkwood. It doesn't make any sense. They're opening diplomatic relations, not conquering or establishing colonies. The whole impetus for his exploration is a misconception...

This is what I'll do. Alright, the misconception was that the ponies were invading the Elkwood (you do know that Equestria is on an entirely different continent, right?), and so he tried to invade it first. Here's my alternative: 

Basically, instead of exploration, Magnus would have decided to secure his place as Sovereign by subjugating the defiant deer on the ground below. He gathered up his best fighters, and began a brutal campaign against the most powerful deer clans. Unfortunately, in true griffon style he underestimated his foes, and after years of hard fighting, his griffons were handily defeated. Magnus himself was afflicted by a disease the deer shamans released among his soldiers, and only barely made it out of the Elkwood alive, with (as you said) a handful of soldiers, compared to the hundreds that left to fight. Disgraced by his loss to the deer, crippled by the Swamp Rot, and defeated in a duel by his own son, Magnus was exiled to Equestria.

It's basically the same outcome, just different circumstances. He would join the Explorers in an attempt to regain his honor, or some such. So, he can still be an arrogant, asshole exiled griffon prince, just not one with knowledge of the unexplored regions of the Western Continent (the continent w/Equestria on it. The Elkwood is across the sea, on the Eastern Continent).

If that doesn't work for you, or if the foreknowledge was what you wanted out of the character, then I'm sorry, but I can't accept him.