It doesn't hijack anything. It took me about 5 minutes to put a NTP client and a web server together in the same sketch. It is running right now. The NTP time is correct to the second, and the server works fine. I used the server code in a function called doServer() instead of loop(), and call it every iteration through loop() just before the NTP stuff.
I used this NTP code:
I used this server code:
http://playground.arduino.cc/Code/WebServerST
It is still running both just fine.
edit: On the NTP code, I replaced the 10 minute delay with a millis() time check so it wouldn't block there for 10 minutes.