I found that adding -Dsun.java2d.opengl=true as a runtime parameter took the 2d viewer from 5fps to 30fps average.
How to do it?
1. Open the Java Control Panel.
You can do that by either launching it from your desktop enviroment or by running jcontrol from terminal.
2. Go to Java Runtime Enviroment Settings.
Look for a View button under Java tab in Java Control Panel.
3. Add -Dsun.java2d.opengl=true to Runtime Parameters.
4. Restart.
I tried running it right after I added the line and after relogging into my desktop enviroment but it only took effect after I rebooted the machine.
I know this isn't the best way to do it as now every Java application starts with opengl enabled 2d acceleration but in my case it actually fixed similar issues with other Java applications I'm running so it isn't a problem.
I'm sure this can help Windows and Mac users as well but my issues were Linux specific as the 2d viewer on the same machine worked fine in Windows 7.