In an upcoming campaign, my players will face a Daemonic Cruiser. It will be a Thunderhawk sent at them and when they destroy it, the shards will transform with energies from the Warp into a full Daemonic Cruiser. Their Explorator npc tells them that he can modify a salvo of Jovian Missiles with a device to banish the daemon, but it will take an hour (2 turns) to do so. This weapon cannot be fired until then. This leaves them with Disruption Cannons for two turns. What effect if any would it have on the sorcerous power and components of a daemon?

Thunderhawks are... quite a bit smaller than Cruisers. There's rules for the Eye of the Abyss somewhere, a daemon-possessed Cruiser. Might be better that destroying the thunderhawk, if you insist on having that happen, completes a summoning ritual that drags the Eye free of the Warp to beset the players?

That would be the basic concept. The players are in pursuit of a strike cruiser called the Cruelty of Fate. Yes, they could stop and do battle, but they are on a mission. So they kick out this simple, easy to destroy ship and it's destruction brings forth a daemonic ship with rules based on the Eye of the Abyss. They can destroy it in (read banish it back to the Warp) in two turns, but in the meantime can the Disruption Cannons slow it down at all? They only have Disruption Cannons and a Jovian Missile Battery. The missiles will be modified with a scratch built device for a single salvo by a Explorator who was branded a Heretek (for free thinking).

Needs more tech-heresy! Modify the macrocannons for airbursting chaff explosions! Melt down the blessed aquilas in the ship for ammunition that forces the daemon to plow through shards of metal that tear at its very being or turn away to avoid them!

Really though, I'd give it some manner of crazy-high regeneration of hull integrity that's only counteracted by being hit by blessed weaponry. Given that it's not a proper ship at all I'd say that a regular disruption effect wouldn't work. If the ship has a Missionary PC, have the heretek suggest that the wavepatterns of the disruption be adjusted to reflect the litanies of hate that the Missionary utters, blessing each shell. It'll only require that the Missionary do this one simple little procedure first... Hits should make it harder to fire its weapons, maybe reduce its speed as well. If I were running this, I'd definitely have the daemon vessel as a chase sequence in a dense asteroid field or gravitic anomaly field or something. Play up that their weapons are doing nothing, the ship is gaining on them, there's a slavering horde of living daemonic ammunition slamming into their hull and tearing its way in to the ducts, and they're moments away from impacting against an asteroid the size of a battleship. Play it out a bit, let the players panic and try to come up with something. Bonus points if you can get them to do what you intend without spelling it out for them.

Pretty much that'd be it. A desperate battle against a daemonic cruiser while the strike cruiser slips away to search for something in derelict ships.

Once the daemon is banished, then it's time to play tag with the strike cruiser to discover what exactly they are looking for and try to destroy it.

No...no Missionary on board.

And the setting for these battles? The Processional of the Damned...a scroll case sealed by psychic powers is hidden in an ancient vessel. Leading to the next clue that eventually leads to a powerful artifact. The Black Legion desires this artifact for it will allow them to conduct a Black Crusade unlike any other. The players desire it only because it will draw the strike cruiser to them for a sorcerer on board is trying to use his powers to track it as their Auger systems are waaay out of whack.