That depends on how many GV's have spawned for HQ.
It's relatively easy to get the V base back. If you already have GV's shelling HQ, you don't have long until the lights go out.
Honour the threat.
It's usually a fair drive to the HQ from the spawn, so If you kill the existing threats, get the V base back then go clean the ones who have re-spawned up, threat eliminated.