Actually, assuming the Doctor doesn't change his personal timeline somehow (or someone else does), you can make sure he won't spoil your deeds ever again.
If he shows up and doesn't know who you are and THEN you kill him for good, you can be reasonably certain he won't show up for you ever again.
Otherwise you have to trick him first into syncing diaries... If he still had meetings ahead of you... not time to kill him yet.