The Java 6 Plug-In is supported with R8 as of M040, so one solution would be to move to R8 M040 or M050.
For Java 6 Update 10 and higher in MSIE 6 and higher and Firefox 3 and higher specific applications can select their own specific Java Plug-In versions and each application will get its own version without conflicting with others as in older versions. This only works for Java 6 Update 10 or higher JVMs to the best of my knowledge, though.
[As someone else noted with R8 M050 one can also run Java 5 on the server for better performance, monitoring, etc, but that's a separate and unrelated decision point.]
As noted on the R8 M050 platform matrix there are TAN's/TPI's on getting Java 6 Update 10 and higher to work without unchecking this option (which generally provides greater stability, higher performance, etc).