Two things:
1. "Clever cheaters...are causing stalemates when they are in bad positions."
Yeah, no. A swing and a miss. In all actuality, "clever" cheaters don't only force stalemates (though they certainly can); they simply cheat on every other move and in every other game, rather than all the time, so it's much less obvious.
2. Adding onto the above: It is not "cheating" to force a draw in an otherwise worthless position. If it was, it would have been eliminated at least a century ago, or there would be a serious debate about it at the top level of players. However, since nothing of the sort has happened, it's pretty clear where they (and everyone else) stand on this issue. (Or, more simply, it would not be encouraged by the official rules of the game — but it is.)
Bottom line: there is no "stalemate controversy," unless you count a vocal minority of butthurt buffoons who suck at checkmating in a position that's otherwise completely winning and then get mad about it, acting as though it's not 100% their fault. The rule is fine the way it is; and unless something truly bonkers happens, that is not up for debate.
Simply don't allow stalemating moves to happen. I really don't like the idea of someone who is 12 points ahead being robbed of a win, even if some consider it a good part of the game on the sole basis awkward positions can occur and it's impossible to tell if engine advice was used to cause the stalemate at that point of the game. I abslutely assure you the clever cheaters aren't winning games, they are causing stalemates when they are in bad positions. There's no way to stop this without stopping stalemates being legal moves.