"Why did they put it there in the first place though?"
Simple. The NSA does not (in theory) work for itself. Such attacks are a policy decision.
And if the policy changes you have to be able to shut it down.
Likewise if you target a group of businesses in order to gain access to an installation once inside and spreading any further infection is unnecessary. Ideally you want the other copies to also self destruct to prevent hardening against them (or perhaps having them used on yourself?)
The documentary "Zero Days" on Stuxnet mentions this stuff briefly.
Biting the hand that feeds IT
