When Nova Prospect blew up I guess it would be good for the resistance but what about all the people that where in the pods? it would have helped to have helped to have a few hundred more rebles.
Well given the sort of situation Gordon and Alyx were in, being completely strapped of time, they obviously did not have the time to go about freeing everyone, plus they knew their only way out was through the portal, which would have taken A LONG time to teleport all of the rebels. Plus it was like a signal for the rebel uprising, no more perfect signal in my opinion, the destruction of the most feared and evil place the Combine contain in City 17.
Also, although this might be wrong, i dont think they actually meant for Nova Prospect to be destroyed, i think when Alyx and Gordon were getting ready to teleport and the elite combine troops burst in and start firing at them, i think that causes some sort of chain reaction that destroys the facility as they teleport away, i may be wrong but meh
And besides, it would be very hard to free all of the people as the combine would send lots of troops, so even if the whole resistance would try to free, they couldnt do it.
I think that if they tried to save them the mind control program (programmed into their brain) would've taken over too soon... so not only would you be dealing with reenforcements, you'd be dealing with new combine soldiers and More troops...