Another thousand died in the next few days before the Capital calmed down a little.
I believe it was the Federation's heavy handedness and willingness to execute all of the spies, agents and traitors that delayed the war by so long.
That particular operation probably blinded our enemies for a good period of time, and allowed the Federation to finally openly act out against ALL of its suspects.
You think all of the thousand who died in the following days were involved in the Slaughter of Zhang Du District?
A generous estimate would probably put the number directly involved at around fifty people.
The other nine hundred fifty killed were mostly family members and suspects that the Federation had placed in its watchlist.
Sometimes, it is good to leave a spy that you've already identified alone. Better a spy you already know, than a new spy whom you do not know at all.
That way you can watch him and know what he's actually after.