After reading some of the fluff in the Grey Knight codex I had this scenario idea:
In the codex it says that the Grey Knights have some secret arrangements with various xeno races that supply them with some of their most exotic anti-daemon equipment. Enemy of my enemy, the greater threat and all that stuff.
What would happen if a Deathwatch kill-team was sent to exterminate the last remnants of one of these xenos races? These xenos are the only ones capable of crafting a particularly valuable piece of equipment, and faced with imminent annihilation they call on their Grey Knight allies to protect them. The Grey Knights intervene, but the arm of the Inquisition that gave the kill-team their orders knows nothing about their secret pact with said xenos: the kill team has already been sent and there is no time to abort the mission. The Grey Knights strike team has only one choice left: kill the Deathwatch marines before they reach their precious "allies".
Or maybe, the Inquisitor that sent the kill team does know that the xenos have an arrangement with the Grey Knights, but he's a puritan extremist who firmly believes that any form of consorting with xenos is heretical in the extreme, even for Grey Knights: if the kill-team has to kill Grey Knights to complete the mission, so be it.