First of all, the boarding operations might seem pointless when the Donnager will probably self-destruct anyway, but as Holden muses in Chapter 15:
Boarding a ship was one of the riskiest maneuvers in naval combat. It was basically a race between the boarders rushing to the engine room and the collective will of those who had their fingers on the self-destruct button. After even one look at Captain Yao, Holden could have told them who'd lose that race.
Still. Someone had thought it was worth the risk.
So, assuming Holden is right, the boarders knew that the most likely outcome was that the Donnager would self-destruct, but that they could also possibly take the ship.
the later development
Just so it's clear what we're talking about, I assume you mean this development:
The plan is to destabilize the solar system by creating all-out war between all major factions through a series of false flag operations. It began with the destruction of the Earth-owned but Belt-staffed ship Canterbury (which of course also supplied the Belt with life-critical resources), which appeared to have been done by Mars. Mars is by far technologically superior to Earth and the Belt/OPA.
So, if the boarders take control of the Donnager, they control a Martian ship and can continue with their initial plan which begun with the Canterbury: Blaming Mars.
If they don't, and the Donnager self-destructs, they know that Mars will probably blame the Belt/OPA for both incidents, which is what happens.
Either way, they achieved their goal.