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.