The terms of Bacco's deal with him were that reporter Ozla Ganiv would allow him to retire -- not resign; retire -- from Starfleet and not publish her expose on what she (Ganiv) believed to be Ross's assassination of Zife (remember, Bacco and Ganiv don't know about Section 31) or his forcing of Zife's resignation at gunpoint, in return for Ross never, ever, ever having or wielding any sort of military or political influence in any way, shape, or form ever again.
In other words, the deal is that Ganiv keeps his secret and doesn't risk war with the Klingons and Bacco lets him escape justice, in return for never doing or saying anything important for as long as he lives.
Well, Section 31 might.
But, no, the point of the deal in Articles of the Federation was that Ganiv wouldn't publish her expose and therefore risk a war with the Klingon Empire. The issue was not what would they do to Ross, but would they release information that would provoke the war that Ross had Zife removed from office in order to prevent.
You are forgetting how the actual sequence of events worked:
Picard, Ross, Nechayev, Paris, Jellico, Nakamura, and the Federation Ambassador to Tezwa (whose name I can't recall) discovered that President Zife (and his COS and Secretary of Military Intelligence) had engaged in a criminal conspiracy to smuggle Federation weapons to Tezwa in violation of the terms of the Khitomer Accords, and that they had subsequently refused to warn the Enterprise or the Klingon fleet when said fleet entered Tezwa orbit, leading to thousands of Klingon deaths. Subsequently, Zife and company ordered the conquest and occupation of Tezwa, leading to millions of Tezwan deaths and thousands of Federation deaths, and engaged in a conspiracy to obstruct justice by trying to plant false evidence to implicate the Tholians and Romulans in the pulse cannons' construction.
It was Picard's, Ross's, Nechayev's, Paris's, Jellico's, Nakamura's, and the Ambassador's judgment that Zife and company's crimes were too great to allow them to get off scott-free and continue in office. But they also believed that a public airing of their crimes would empower the reactionary anti-Federation faction in Klingon politics and lead to a devastating Federation-Klingon war.
Therefore, Picard and company engaged in a conspiracy to force Zife to resign at gunpoint.
Picard and company did not engage in a conspiracy to kill Zife. Rather, Section 31 discovered that Ross was part of a conspiracy to force Zife to resign, and they took advantage of the situation; Ross conspired with Section 31 to have Zife, Azernal, and Quafina assassinated after resigning, without the prior knowledge or consent of the other members of the "resign-at-gunpoint" conspiracy.
No work has yet established if Ross agreed with or willingly participated in Section 31's assassination of Zife, Azernal, and Quafina, or if Ross was coerced into abetting their assassination.
As for how Section 31 kept Zife's death a secret -- when you think about it, it actually shouldn't be too hard to fake someone's non-death if you have Section 31's resources. Give someone cosmetic surgery now and then to make public appearances (or use a hologram); upload a few property deeds in Zife's name on some remote resort colony planet, and file an annual tax return in his name; etc. Make sure your Fake Min is on hand to use a shovel when they break ground at the Min Zife Federation Presidential Library on Bolarus.
And of course the Borg Invasion represented a perfect opportunity to just simplify everything by reporting his death in the invasion.
