Hi Peter,
Such a performance hit is definitely not an expected behaviour.
However, performance issues are not very easy to solve without a clearer information about your configuration and JRebel logs.
First, enable JRebel trace and performance logging with these two arguments:
-Drebel.log=trace -Drebel.log.perf=true
Then restart your application server, deploy the application and run it until you come across the performance issues. When you have, then you can zip the log file and send it to us at support@zeroturnaround.com
Along with the log file, tell us at what HTTP request the delay happened and also tell us a bit more about your setup(app server, debugger enabled/disabled, etc)