The concerns about Deathwatch fighting non-Xenos wouldn't be so big if GW had actually released the Alien/Xenos Hunters Codex.
Afterall, the Witch Hunters and Daemonhunters books both include a 2-page spread of reasons their faction might be fighting each race; including Witch Hunters fighting Xenos armies and Daemon-focused Chaos armies, and the Daemonhunters fighting Xenos for reasons other than "their leader is possessed by a Daemon etc".
As others have said, its perfectly fine for the Deathwatch to be assigned with non-Xenos-killing assignments if they're the only group in the area able to help.
Also, the Deathwatch might be serving under an Inquisitor working with other Ordos because their goals are related.
Scourge the Heretic and Innocence Proves Nothing (Dark Heresy novels), the main group of Acolytes (from Ordo Hereticus) are trying to hunt down rogue psykers and heretics, who are in turn being aided by a group known by the Faxlignae (not sure if that's the right spelling) who use Xenos tech. This in turn has the acolytes eventually working alongside an Ordo Xenox Inquisitor who has a Deathwatch team under his command. Also, an Ordo Malleus Inquisitor is asked to help because the Hereticus acolytes believed they had fought some Daemons along the way.
This very example shows Deathwatch working to aid in matters not necessarily related to Xenos directly, and while the Faxlignae are their target, they end up fighting nothing even remotely Alien.
Its also possible that maybe something believed to be caused by Xenos are actually caused by something else (maybe Tzeentch cultists are leaving misleading evidence to throw off any Grey Knight pursuit), or while in-between missions (or even on one), they are caught in the middle of a conflict due to Daemon incursions, heretical uprisings etc.
Just a few ideas.