Can you not convert them as and when you want to move them over to your Kobo? You can convert just before you send the books to your device.
I'm getting a GLO for Christmas and as a current Kindle 3 owner, I've been making sure to covert the books in my Calibre library I know I'll move straight away. I just left it running in the background while I did other things.
I've also been making sure to grab both mobi and epub files for any new books I've bought since I decided I really wanted a Glo. I've chucked them both into Calibre so I have both versions saved in the same book title to try to make sure I am Glo ready.