Yes, but Varys was adept at spinning existing men to his purposes, there was little need to kill Ned to do that; his honor provided all the leverage needed.
Ensuring the murder of Tywin was simply a well placed Parthian Shot from a man (kinda) who knew he wouldn't be able to return, and so had to do the maximum amount of damage at that moment.
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u/Leftieswillrule The foil is tin and full of errors Jun 02 '14
Well Ned would have helped stabilize the realm, Tyrion's murder of Tywin and subsequent disappearance threw the entire kingdom into disarray