Well they will eventually won't they? The shipyards will eventually be reconstructed (probably somewhere else as the location is no longer secret enough to be secure). However now the rest of the Alliance are presumably aware of the project to build a destroyer class whitestar, the original shipyards for the whitestar fleet may be usable.
The big question is probably whether the end product will look anything like the Victory class, or function likewise. Will the new destroyer be more efficient if the new designer is not compromised by the Drakh or anyone else?
I don't think the main weapon difficulty will be resolved, that's a bridge too far with the tech available.
Some systems in place on the whitestar seem to be missing from the Excalibur, how much of this is due to practicality, and power distribution problems, and how much is down to wilfull neglect. The organic armour is gone, as is the minbari "curtain" style main viewer.
The Excalibur seems to be designed for rapid response missions. It is fast, and packs a punch, it's armour is enough to withstand the firepower of your average alliance vessel and it can probably take a fair bit of punishment in a fair fight. It was probably intended to be used primarily for policing Alliance territory, acting as a c&c vessel for whitestars, and being the back up in an assault.
With known malevolent forces out there, the needs for an alliance destroyer may change or adapt, they may prefer to lose the ambitious idea of incorporating vorlon weaponry, and stick with the defensive aspect of the vessel, the power necessary may also shave off some of the speed aspect of the destroyer. They would probably look in to developing a varied task force of destroyers, each with differing levels of strengths in the aspects of defence, speed, firepower and scanning.
This is all just my opinion though. /forums/images/icons/wink.gif