The problem is you gotta be nearby the starbase. If you're 2+ jumps away and he's brought his own small fleet with it, you're screwed.
He's free to take pot shots at you as you destroy the starbase OR his starbase makes it because you spend your effort killing off the fleet first.
If you're right there and can get to it as it starts, sure, counterable.
But that's not the problem. The problem is it takes a long time just to get to it while it's being constructed.