I really don't know how often a situation like that comes up. You'd have to be looking at A) a temporary call-up situation (if it was permanent the salary issue is obviously moot) B) having 2 different players that could fill the same role and C) one of those players having already been called up earlier in the season to be making big league money (or I guess you could have stashed a vet in AAA).
But, like I said, I don't really care either way. My only statement is that it is how it works for guys with minimum contracts and options in real life, so it would make sense if they put it in the game. But we're talking about a difference of 300K or less, so it's a big deal for someone, they probably have issues elsewhere.