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Originally Posted by
Tergon
We haven't seen them using time-travel, but they may have access to that technology. The whole point of the Silence is that you don't know they're there unless you look very, very carefully, or if they want you to be there.
It could simply be a pragmatic thing, as well. They haven't bothered to interfere with the Doctor aside from killing him, because if things can be rewritten and the timeline changed, he could repair any of their other shenanigans.
In their position, it makes sense to deal with the source of the problem first. Don't blow time and resources on changes to the timeline that could be retconned. Instead, kill the Doctor and erase the last Time Lord from existence, and then you're free to make merry hell with the timeline knowing that he can't retroactively stop you. He won't show up anywhere that history doesn't say he does, relative to them, which gives them a free hand to do as they please. They just don't make a move until then.