I also worked on a project that used ClearCase with Eclipse. The same drama that you described happened to us on a regular basis. ClearCase was a big part of my reason to quit this job.
With some distance between me and this horror, I came up with a possible solution. Set up several different Eclipse installations with not only separate workspaces, but also separate .metadataand related things. Go into separate eclipses from different views, then turn off one and launch another to work with another view.
I have not tried this, but it seems to me that this should work.
Oh yes, you want to export your settings between Eclipse installations.