It is possible to integrate some containers like
Tomcat with the Apache Web Server, allowing both server side
Java and CGI or other popular scripting languages such as PHP to be run at the same time from the same domain.
After that, all someone here can say is that it depends on the code.
CGI is fundamentally different from servlets and JSP.
Things like logins, sessions, concurrency issues, etc would need to be worked out. Without digging through what's already there, nobody on a forum or user list will be able to tell you with any degree of certainty how easy or difficult this will be.