Is GSX supposed to 'lock' the gate once selected or is deletion of an AI aircraft the only option?
There's no interaction whatsoever between GSX and the default FSX ATC, they are entirely unrelated.
If some AI go to the parking you have been assigned to by the FSX ATC, this would have happened regardless if you used GSX or not, and it shouldn't be happening in the first place, because it would be the FSX ATC that should "lock" your selection from being assigned to other AIs. GSX doesn't have anything to do with this interaction.
If, instead, you select a parking in GSX that is not necessarily the same you have been assigned by the FSX ATC, there's no guarantee the FSX ATC won't assign it to another AI by the time you get there, and GSX won't do anything to prevent it. The only thing that GSX checks for, is if a parking is *already* taken by an AI when you select it, but it's not constantly monitoring it or trying to "kill" any AI that goes there.
In this case, you either remove the AI using some kind of external tool, or you just request another parking to GSX as soon you realize yours has been taken, which seems to be the more realistic option.
