It looks like Eclipse in silence have created a fix and announced it in all secracy through their wiki (!). It seems to alleviate the problems for me at least; though I have not tested it in length yet.
See http://wiki.eclipse.org/Platform_UI/Juno_Performance_Investigation
Basically you should install the “Juno SR1 Patches/Eclipse UI Juno SR1 Optimization” from their 4.2 update site: http://download.eclipse.org/eclipse/updates/4.2
Bug-tracking for this optimization: https://bugs.eclipse.org/bugs/show_bug.cgi?id=394588