PC's are in the process of killing an important story NPC, whats one to do?

[Hatchling Dragon]

You could always have the reinforcements show up 'downstairs' (or wherever would be appropriate) and make enough noise to let the PC's know they're there. Make sure that they show up in such a way that the PC's have an avenue of escape.

If this was the head of the Guild of Thieves then he'd always have some backup off-site just in case. Thiefs are smart critters, they're going to have contingency plans within backup plans.

Now, if they CDG him before leaving then I'm out of options unless you want to ressurect him.