I think it's not so much what Phonak wants to do, as it is what the other teams won't do. When you're in yellow, like it or not you're the top team, and other teams will not help you.
CSC and Rabobank might have the same goal as Phonak, but they won't help the team with the yellow jersey unless they absolutely have to, or unless they give up on first place and start defending a podium spot. So, Phonak will end up working unassisted.
Let's say Andreas Kloden goes on the attack tomorrow - Phonak will have to chase to limit time losses, but Rabobank and CSC might just sit in and figure any shakeup is a good thing. Let Kloden and Phonak tire each other out, we'll wait till tomorrow to strike.
This year's Tour is just so crazy, with so many top favorites out, that the yellow jersey is like a hot potato. It's good to be a wild card when you're playing chicken - nobody knows what you'll do, or what you're capable of. It's bad to be the favorite, because nobody's going to help you.
It may have been tactically smarter for Floyd to have let Dessel keep the jersey for another day, but I think once Kloden et al were dropped, he had to ride as hard as he could to take time out of them.