He might have been unhappy, sure, but I've been of the opinion that while Sideous had a lot of plans for Anakin, he wasn't 100% necessary for his plans of galactic domination. Palpatine's a smart man, and I think he knew better than anyone that with the type of lifestyle Anakin had (being a Jedi), he could die at any moment, any number of times, and there isn't really anything Palpatine could do to prevent that.
So if Anakin ended up getting butt****ed by Dooku and died, well, "that sucks". But the plan would continue.
I mean, when you think about it, Anakin never even really played a pivotal part in the Empire. Even without Anakin, the 501st could have sacked the Jedi Temple. Even without Anakin, Palpatine still had the emergency war powers to control the military. Even without Anakin, he still had the massive power of the Empire to control the galaxy.
TL;DR: Post-PT Vader, and Sideous' reaction to Vader being what he is (a shell of his former self) answers your question pretty well.