Well, you're right Irvy
, as far as it goes.
But the point of the Silence's plan wasn't to just kill the Doctor in general. It was to kill the Doctor before has the chance to do a specific thing
They knew that he would do this business on the Fields of Trenzalor or whatever at some point - they probably know that because as you say, the Doctor is a time-traveller and that event could happen at any point in objective time
But they also knew that he hadn't done it yet from his own point of view, in the Doctor's subjective time
. If they could kill him before he got to that point in his own personal timeline, then that one event would be averted, and presumably whatever other side-effect timeline changes resulted from that were worth the risk.
So yes, killing the Doctor doesn't mean he won't still show up to do something
. But it does mean he won't show up to do this particular thing