This is my view:
If the standard should be changed so that the player with the highest WAR is the MVP then the MVP as an award would become outmoded.
If WAR is to be considered the single indicator of a league MVP, there is no need for consideration. MVP titles become something of a universal mathematic truth. If the MVP title is to remain an award, then I think it's perfectly acceptable for a man who won the triple effin' crown to be considered the best player for a given year.
Why are these awards handed out every year? Because there shouldn't be a consistent mathematical outcome which determines a player's worthiness, a purely subjective consideration. If you're upset that Trout didn't win the MVP, consider that winning something is different than earning something.
Trout earned the respect and admiration of baseball fans because objectively he's the best offensive and defensive player in the American League. Cabrera won a silly plaque. Who cares?