Hi Markus,
Hmm no I'm afraid this is not possible ATM, we didn't have that use case in mind
when developing the filter. Might be a nice addition though.
You case wouldn't be just about translations of the categories, would it?
If it is, you wouldn't need two trees, see
http://taxonomy.forge.onehippo.org/category-localization.html
HTH
Jeroen