I'm not sure I followed all the way along in the scenario, but here's my attempt...
1. You have a game with 1 second on the clock
2. If team B made both shots from the intentional foul, they're now up 3 points
3. Player from A comes across the throw in plane and is warned.
IMO, if you don't stop player A from doing this again it would be wrong. It's possible (if I have the above facts right) that pressure from player A causes a bad throw and someone from A grabs the inbound, chucks a prayer-3 pointer that ties the game. (Maybe not probable, but possible.)
So, you have to do something about the throw in plane violation. Your choice to warn again or call the T (although by the rules it's a T). I think you were responsible in the way you handled it.
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