How do we know it was a one time thing by Starfleet?
Because we're the audience, which means we're as close to omniscient as possible.

We've heard those characters' internal monologues and we know their motivations in a way we would not if we were characters in the story. No one in Starfleet has any intention of doing that ever again.
When dealing with the possibility of war should the Federation not be doing what it can to reduce the risk as much as possible? If (when?) word leaks out about the Federations actions on Tezwa, the Klingons may react much more strongly to what they would see as the dishonourable way the Federation attempted to cover up their actions. That's something that is more likely to lead to war than the actual Tezwa incident.
I think there's no reasonable way to predict Klingon behavior at this point. The Kopek faction is gone, and Martok seems to be ruling the Empire virtually unchallenged, but it's hard to say how the Klingons will react as a whole after having gone through the Borg Invasion.
Worf knows that something has happened and he's got a leg in both camps. The man he considers a brother is the leader of the Klingon Empire after all. What happens when he starts questioning what he hears? He's Picard's first officer. He's got access that almost nobody else does.
But the fact remains that Worf, though he knows that Zife resigned because of the Tezwa debacle, does not know that Picard, Ross, and Company forced Zife out at gunpoint. They didn't leave any evidence of that behind.
I find it unlikely that nobody is questioning Zife's disappearance along with the Secretary of Military Intelligence and Zife's Chief of Staff. Did they all just go on vacation somewhere? Did someone create a false report that they were all killed in the Borg invasion? Too many loose ends and too many people know something has happened to them.
Ozla Graniv of the Trill newsmagazine
Seeker eventually realized that no one had heard from Zife and company after their resignations. That's what led to her investigation. No other reporter seems to have begun investigating anything. As far as what's happened beyond that, nothing's been established. But author David Mack did write on the Psi Phi Bulletin Board that if he were to re-write anything he'd had published, he would insert a section into
A Time to Heal indicating that Section 31 was using a hologram or impersonator to make appearances for Zife so as to allay suspicion. I consider that as good as "canon" for my personal use, but your mileage may vary.
In the wake of the Borg Invasion, there's no really any need for anyone to fake a report of his death. He can just be listed as missing, like most of the other 63 billion dead.
ETA:
Sci, Bacco's scruples mean little if when the time comes to use them, Starfleet steps in and acts like the military of a banana republic. The Federation acted worse than is expected of civilized nations today, in the real world. You seem to think that only "saints" can be expected to act as they previously agreed to.
No -- I'm just a bit more forgiving of Picard and Company's decision to remove Zife at gunpoint because of the very fact that, as an audience member, the narrator has told me their internal monologues and motivations, meaning that I know and can therefore trust their intentions far more than I ever could in real life. If I were a character in the novel, rendered ignorant of Starfleet's motives and intentions, I certainly would be far less forgiving, because I would have far less reason to think them trustworthy.
But in this instance, those Starfleet officers acted to remove a war criminal from power in the only manner they believed likely to avoid a war. This wasn't done out of power lust, or a desire to subvert democracy, nor was it done eagerly. It was done out of a reluctant desire to prevent a war criminal from remaining in power -- which is not an unjust motivation.
I see it as the equivalent of Johnny Smith in the novel
The Dead Zone having a vision of the future that a presidential candidate would cause a nuclear war and choosing to assassinate him beforehand. Certainly, in real life, if presidential candidates were being assassinated, democracy could not function. And certainly, in real life, I would not trust anyone claiming to have visions of the future that must be acted upon to avert such fates. But in the novel, we know that Johnny's visions are reliable, we know that Johnny is not mentally ill, and therefore we know that his decision is just. That it is a work of fiction alters the parameters of evaluating the characters' morality and trustworthiness, because we are rendered omniscient in a way we could never be in real life.
If there are no repercussions, without oversight there is no civilization. Zife got elected by people who gambled on his being right for the job. If they never find out he wasn't, they'll elect another like him or worse
The final
A Time to... novels made it very clear that Min Zife's approval ratings had utterly collapsed in the wake of Tezwa. The man had no public support anymore -- people had already soured on him before his resignation.