That would be easy to combat! Increasing the time it takes to build them would be crude, but it would work. Otherwise, perhaps having them require both an engi bay and factory to make? Or potentially even incorporating them into the ghost academy - they do seem sort of covert - not your simply rax soldier. Thier speed upgrade already requires a factory, so perhaps they could be built at a factory, or further incorporated into the factory?
Another idea would be to reduce thier speed significantly (to about marine speeds) but make thier upgrade speed the same as it is now (with the upgrade). Also, making the upgrade more expensive and take longer (since it gives more benefit). Potentially the upgrade could be at a factory tech lab?