I agree that Mylyn should be able to pull environment variables into a commit message but I don't think it's currently possible.
I looked at the Mylyn source and docs and couldn't figure out a way to accomplish this within Mylyn directly, I think you're only option is to create a SVN hook/trigger that would either expand the environment variables for you or inject them at specific location within all commit log messages.
For reference I checked out a copy of the code base from here: http://wiki.eclipse.org/index.php/Mylyn/Contributor_Reference#Active_branches