The external program could try and "detect" known cheating programs like Ultrawarp and whatever is being used these days. Bit like those UTSecure and stuff use to do on UnrealTournament, where the mod ran on the client machines and checked if the known cheating programs were running. And if they are detected, even disable itself, or alert in game. Not 100% secure, but would stop the casual cheating that goes on.

And like it could keep a note of the players position, and detect if the pos changes suddenly without reason. Though I guess it would need a way to detect legal warps (eg warpzone in the level).

I'm not a programmer so I have no idea whats possible, but going from conversation from Overlord and looking at current programs out I dont see why this wouldnt be possible, though a lot of work.