Yes you can have multiple version of java on the same machine.
Your environment problem has its challanges. I'd suggest setting the default JAVA_HOME to be the 1.4.1 for all the tools, etc... and create a shell script called 'dbshell' or whatever and have it spawn a new shell and set the JAVA_HOME to the IBM Java. You can also change the prompt so you dont get confused. When you are done running the db tools, you can exit, and be at the point were you before launching the dbshell.
good luck, not an easy problem to work around.