Heathen!!
Deamonhunters sort of give it away in the title >_<. They don't go around protecting the Imperium for any old reason (thats what guard and SM are for). They are above petty wars, they fight the great enemy and to this end the do come in contact with other races occasionally. See pages 52-53 in the DH codex and it comes up with a plethora of reasons that you can expand into a narrative easily.
As for the size of your force, well GK only go to war on a large scale once every century or so so not having a big force is no problem. Mostly you would see Grey Kights allied in to other army's to add their experience or following an =][= who has asked for their aid.

PL

 

O.O jeez ok they will hunt daemonized tyranids and well dark eldar are witches anyways, and well the way i see it a grey knights not gonna say let the xenos scum live anyways...

i know the codex has narrative things it just im more worried about my friends because it forces them to follow MY sides narrative...

any idea PL?

oh and thanks for the plethora of advice so far dude keep it up and ill see if i can freakin force ppl to give you rep!

 

Well.. One easy option would be to make up some daemon related objective which would involve fighting all those other forces but without always having daemons involved.

Like, say, if you're fighting over a series of planets.. Maybe there are a series of shrines spread across these worlds which contain the essence of a powerful daemon who must never be released, or perhaps some artefacts or rituals need to be gathered and performed there to prevent some great daemonic catastrophy (5th Element style.) So the Grey Knights need to secure these areas from the Xenos and others who might be trying to hold it. Even lesser forces like guardsmen or mundane space marines might have to be eradicated if they get too close.. You can't trust them with something so important.

 

or you could do ordos Xenos using demonhunter count as with help from Death watch. that way your fluff is a simple purge of all things alien

 

Another possible idea is perhaps these planets are trafficking in warp and xeno tech. Granted that xeno tech might belong to the Ordos Xenos, but if a Daemonhunter is the only Inquisitor there, then congrats he gets the paperwork.

It could also be this is the planet system the local Inquisitor Lord resides, I mean that's the beauty of naratives, pretty much anything is possible.

Though we're gonna have some problems if a lone Inquisitor with no retinue takes down a Avatar of Khaine and Abbadon the Despoiler in one round of combat each.

 

Grey knights might not stay around to defend a world from say, orks (they will be needed elsewhere), but an Ordo Malleus Inquisitor might stay in an area which isn't directly related to Daemons if he felt it would serve the Imperium and no one else was around to save the day.

It isn't inconceivable to imagine an Inquisitor Lord, having completed an extensive purge of an important Agri-World's government, staying to defend the same planet from ork pirates which have just arrived if the planet didn't have a dedicated PDF.

If its within the Inquisitors power to save the world using storm troopers or inducted Imperial Guardsmen he isn't going to abandon an important world just because his opponent isn't a daemon (a backwater planet might be a different matter though).

To give you an example I recently Games Mastered a Dark Heresy game where acolytes of an Ordo Hereticus Inquisitor investigated strange goings on on a Hive world. Turned out that rather being a psyker the enemy was an alien. Rather than walking away and calling the Ordo Xenos the PC's continued the investigation and destroyed their adversary.

Its worth mentioning that technically some Inquisitors don't actually belong to any Ordo or belong to an obscure Ordo (such as Ordo Sicarius).

Also bare in mind that some planets are home to renowned (and feared) Inquisitorial fortresses. Inquisitorial forces based on such planets might lend their support to a particularly dire threat such as an Ork Waaagh even if didn't directly fall within their sphere of influence.

Basically try to differentiate between Inquisitors being sent to combat a particular threat and Inquisitors being the only servants of the Imperium in a particular area.