He only said that to further erase what's left of Anakin's loyalty to the Jedi. Palpatine knows that his appointing Anakin as personal representative of the Jedi Council would make the Jedi distrust him even more and they made that clear by denying Anakin the rank of Master. Once that happens, Anakin will hate the Jedi even more thus driving him closer to Palpatine's grip. Palpatine was not completely honest because he didn't explain why Dooku is still dangerous. Dooku lost both hands and is at Anakin's mercy so he's not a threat anymore but Palpatine still tells Anakin to kill him because he knows that Dooku is only dangerous to HIM. Palpatine didn't want Dooku exposing him as Darth Sidious, the very Sith Lord that he spoke of to the Jedi so he had him bumped off. When Mace Windu made that same quote about Palpatine, Anakin should not even compare that to what he did with Dooku because knows that Palpatine is dangerous to everyone...Padme, the Jedi, the Republic, and the galaxy at large but he didn't care because he thinks that Palpatine has the power to save Padme so Anakin helps him take out Mace.