When McAfee is set to scan on read, you do get a big overhead with jar files. This is because (my assumption) the jvm just reads the manifest from a jar file so that it can work out where particular class files are located. McAfee does not see things the same way, so before the file is opened, McAfee scans the entire file.
The simplest way out is to disable scanning on the specific directories containing jar files and classes. You only need to do this when files are read. I don't think anything has substantially changed between McAfee 7 and 8, we have the same problem there. It may be that the exclusions list has not been updated between revs.
We had significant speed issues with McAfee scanning until we placed the jar files and associated Windchill folders into the exclusion window. We found that placing them into the High Risk exclusions area was the fix after testing both High and Low.