Swarzak has been starting in Hendriks place. Pavano, Liriano, Blackburn, Swarzak and Marquis would make five. Waldrop is only on the MLB DL because he was injured, on the 40-man, and hadn't been demoted yet. The minute he's activated, he'll be optioned. Burnett made the team by default, so I would expect him to be optioned. Baker could be moved to the 60-day DL and then there is an open spot on the 40-man.
There are a lot of way to make this work, if the Twins were interested in doing so... in my opinion, Thompson is better than Burnett, so it's really an easy choice to make.