"The Doctor" isn't his name though, and she says that he's hiding his name.
The witches were living in secret hence the power that the name "Carrionite" had over them, was more shock than anything else, "Time Lord" wouldn't have had a similar effect.
Possibly because 'Doctor' is a title and 'Time Lord' is his species. He doesn't seem to have a proper name. Also he's probably just too powerful to be overcome by the witch's "magic".