No, secretly murdering and assassinating people is not acceptable in the name of practical gain for your side, period. Maybe there are some exceptions for extreme scenarios like ITPM where billions of lives are in the balance. But for the cited example of Koval, the goal was not saving lives, the goal was giving the Federation political control over Romulus after the war. It's akin to the way the US aided military coups against democracies in order to serve their oil interests. And the virus would be like winning a war by nuking the entire country.
You must consider Henry Kissinger your personal hero, and consider Cerberus the heroes of Mass Effect.
Well that's quite the long-game you accuse Section 31 of playing. So they knew Koval would eventually bring in the Romulans into the war...they knew they would win the war...and then the real purpose was political control? Was this in the books? I mean I certainty could see where that would be a benefit but I think their interests were more short-term.
I concur with Cerebus, and agree Kisinger was a positive force. If its either nuking the entirety of the other country or being enslaved by the despotic regime of the that other country...at least with the US, I can guarantee you its the former every time.