I love theories about the Destroyer. They make me cackle evilly and look forward to writing the end.
It's called the Destroyer because it's the destruction part of the trinity with the Creator and Preserver. That's sort of the whole point. Changing the Destroyer's name would destroy the parallel between them.
Besides, the Destroyer isn't even "something which destroys" except in a very indirect sense, and since absolutely nothing is known about the Destroyer except that it's something that drains the power of the legendaries and causes the War of the Legends, "the Destroyer" is in fact probably the least obvious name you can give it without making assumptions out of nowhere; I mean, I'd consider "the Power-Drainer" or "the War-Causing One" far worse.
Uh, the Creator/Preserver/Destroyer thing is actually inspired by Hindu mythology, which literally has Brahma the Creator, Vishnu the Preserver and Shiva the Destroyer. And the creatures from Norse mythology that Xerneas, Yveltal and Zygarde are believed to be based on are not actually associated with life, death or order to my knowledge (they're actually very minor characters) - I'm pretty sure that part is all Game Freak's imagination. So no, definitely no connection.
I did laugh when Y talked about Yveltal draining the power of Pokémon over a thousand years, though.