To me still this whole operation, has problems:
#1, Unless the extended Hax clan is all kept close (in which case the attack on Scintilla solves this problem) , those Deaths the PC are looking at could be spread across the sector. Which can mean weeks/months in the Warp. Once I started to off the "legit" heirs who could seize command the title, the clock is already ticking on Scintilla. You shouldn't have that much time to investigate # of deaths and stop part 2.
#2, Stealing the Weapons from a Naval Ship. Even if docked in drydock, should be nearly impossible without the help of the both the Admiral of the ship and the Lord Inquisitor who commands the team in charge of the weapon. Now move the weapons to a storage locker while maintance is being done. And given the bureaucratic nightmare that 40k can be, the security could be limited to "just" the Lord Inquisitor team and "limited dockside security" unless the PC team gets there in time. Then you still have to transport the weapon from the naval yard to Scintilla, but we could have a Rogue Trader for that, one who family might have ties to Malfi, or even better ties to Severan Dominate space for the false flag while Malfi, assumes command of the sector.
As our group doesn't play Rogue Trader, what weapons are available to a Rogue Trader that could be used to "wipeout/put a serious hurt on" a planet or hive?