I'd rather see her exiled, but I can understand the logical reason of killing her off by Dooku. Gives Anakin a reason to be so angry with Dooku in E3.
Although we all know the real reason is because Dooku tried to have Padme asassinated, plus severed Anakin's arm. Making him feel less human and more of a machine-which is kind of a connection to him as Vader from the original trilogy.
~I'm just a SciFi Geek with way too much time on her hands~