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How backstory sound do you think Grey Knights/Sisters/Inquisitors accompanying Blood Angels or Dark Angles on the feild of battle is? I understand these allies joining Imperial Fists, Ultramarines or any other codex marine chapter, but these other chapters such as BA or DA have alot to hide of from the Inquisition. It just seems weird to me to see a squad of Grey Knights or a Puritan Inquisitor on the table fighting along side Death Company or the Deathwing.

Fluff and rules don't always go hand in hand.
Not too suprising...and yes, they are iffy about Inquisition on their turf.

well according to As for sisters I can see them working with anyone provided that their homeworld is being attacked and they then ally with whatever imperial forces are in the sector

Inquisitors are able to outright requisition Astartes chapters to do something for them. While obviously they wouldn't get a full Chapter, certain things may require a company so it is completely possible.

If an Inquisitor was working with a few squads of GK in order to bring down a plot by a Cult group, the Astartes may be called in for extra firepower or even some aid in dealing with a foe, since the GK's cannot spare anymore men as fighting in the Eye is getting worse.

I always thought of Larger forces being a distraction for the Inquisitors as they moved in after a leader or a cult. Kinda how my fluff works for mine. He rides in in a Valk, keeping a low profile, as marines tackle the tougher "targets". Like a sorcerer controlling traitor guard. The SM take the bulk of the force, with tanks and infantry, while the Inquisitor runs in with a small elite force of handpicked troops to take out the leaders and there men.

I can see Dark Angels and Ordo Mallus working well together.

The only issue would be the DA attempting to sneak a captured CSM or too off the battlefield... and if the fighting was spread out enough, then loading them onto the thunderhawk picking up the brothers wouldn't be too hard.

Fluff-wise, it can happen.

Inquisitors can technically sieze command of anything in the Imperium - from entire Imperial Guard regiments and Naval fleets to Astartes Chapters and Mechanicus Titan Legios.

In the latter two cases they are, of course, able to do so in theory... but no sane Inquisitor (which probably rules out most of the flamer-happy Ordo Heretics nutjobs...) would be stupid enough to actually do do. They'd make an insistant request. And any honourable Chapter Master or Legio Princeps would assist..

Now, in the Daemonhunters Codex, it states that you cannot take Grey Knights in an army which contains any other Space Marines. This is an approximation of the fact that 'vanilla' Astartes are hugely rare in the Imperium (despite what GW's sales would have you believe) and are, to most of the populace, a myth at best. The Grey Knights are so, so rare in comparison - that they'd almost never appear on the same world.

A Malleus Inquisitor, however, would fit right in with some Marines. Perhaps he's discovered a dangerous cult on a nearby system and a Company of Marines returning to their homeworld heard his call for aid and have offered their holy bolters and chainswords?

The possiblities are endless...