(This was a comment but I guess it could also be an answer..)
Its a fairly common 'line' in 'thrillers' indicating he does not want a trail of evidence leading back to him - ie. No one must know that Ezra ordered (and made use of government resources to do so) the elimination of Bourne and Parsons (or whatever else Ezra was doing, or whatever evidence the pair had on him also).
In movies like that they (in this case, Vosen) will also be 'tying up the leads', removing other evidence, etc.
In any official enquiry that follows such incidents, there will be no evidence that Ezra had any involvement.
There is nothing related to Bournes actual 'come back' physically.
Related to the film:
Later in the film, it is revealed that Kramer is working closely with Noah Vosen and their contingency plan if the current operation goes sideways is to pin the entire ordeal on Landy and hang her out to dry.
However, when Bourne lures Vosen and his squad out of their office he manages to steal all of Vosen's top-secret documents from his safe, which reveal classified secrets regarding Operation Blackbriar and Operation Treadstone.
The failure of Vosen to either protect or remove the trail of evidence involving Ezra in projects that are likely ill thought of in Washington leads to their downfall:
After he gives the files to Landy she faxes the most critical ones off to a colleague in Washington, which leads to the prosecution of not only Kramer, but Vosen and Albert Hirsch as well.