I found a workaround over on GitHub: https://github.com/jmhofer/eCobertura/issues/8
For those who don't want to click the link, here's the text of the comment:
Good workaround: Create a run configuration with a filter, that excludes everything ("*") and let it run just a single test. Name it "Undo coverage".
I did this and it worked quite well in Eclipse Juno.
Credit for this goes to UsulSK.