I don't think so. To my mind defending against these is just part of the strategy, or using them against your opponents in the same way. Either way, by the time these things are on the field you should have enough resources to get auxilliary government upgrades for a starbase.

I wouldn't mind a superweapon on/off button at the start of a match though.

The Coronata Titan's ultimate has the same problem. You get your Titan to the capital, and it's game over. For capital victory you really need to have a Starbase there with aux government (which hopefully blocks the titan ability and definitely blocks the Novalith).