[Q]

Just to make it clear: allegiance subverters do not work against ships with an intact master computer (and as far as I know they never did). However if the master computer is destroyed first the ship becomes vulnerable to the allegiance subverter. And IMO this is how it should be.
The cost of a master computer is not a real concern for larger ships. So if you make ships even with a destroyed master computer resistent to the allegiance subverter, the psychic trait would loose its main advantage. And all AI empires, who never use master computers, would get weaker compared to human players. And that's certainly not what I want.