I got the Aldiko option as well. I did not have an option to import into the Kobo app. I was able though to go to the Kobo app and import from CC. In app I had the choice whether to leave the file on the disk in CC or to delete it from there and only have it in the appropriate Kobo directory.
I did this on a Nexus 7 running the latest Kobo and Aldiko apps.