This is where MyDNS would be handy, you would just point both DNS servers to the same MySQL database (replicated of course) and let it run, both would have the same zones and records files(so to speak) available. Basically you need to figure out a way to pass from Server A to Server B, the names of the domains to replicate/create in named.conf and let it do it's thing. A simple set of php scripts could do the heavy lifting, but be sure to lock down the security such that only the two machines can talk to each other.
I would expect you would have to at least put a call into the ISPConfig code to run said script however... I'm not sure where, since I've about given up on hacks to ISPConfig 2.x hacks, everytime I do it, I upgrade and forget to back up my hacks..