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I currently am writing a story about stormtroopers and the main thing about the story line is that they were assigned to a inquisitor, said inquisitor got killed, and then they were forced to go rogue as a result of the inquisitor dying in battle in order to avoid execution ... is this plausible or does the inquisition have ways of dealing with the leftovers besides killing them all?

Is this referring to Munitorum Storm Troopers or Inquisition Storm Troopers?

Either way, I don't really think there is much reason in executing loyal forces just because their commander died - unless maybe they saw something they should not have seen ... but even then, the Inquisition has the option to use mindscrubbing techniques, and whilst usually reserved for elite forces due to the resource/time investment, the Storm Troopers may easily qualify due to their relative rarity. Added to that comes their Schola upbringing... these guys have been raised much the same way as Adepta Sororitas and Commissars, so I don't think "going rogue" would be a thought that would come easily.
I could certainly see both conditions being met (some extra-paranoid Inquisitor wanting to "make sure" knowledge is contained + rising dissent within the Storm Trooper team) either way, it's just something that I think has a fairly low chance of happening. That said, this goes for a whole lot of 40k stories, so meh.

That's all just personal interpretation based on what I read in GW material, though - sources you do not have to stick to. There have been Black Library novels that completely go against the ST's established background, and when BL writers are allowed to deviate from GW's vision so much, then you are, too. It's up to you how close you'd want to stick to the stuff it says in the codices etc.

I thought there was just munitorium stormtroopers and they were sent out into the field and if needed called to an inquisitor

Nah - but an Inquisitor can also call upon the Munitorum Storm Troopers if need be, I think. Usually this would happen if both are already on location, for when an Inquisitor attempts to call in backup from elsewhere, he may as well get a squad of ISTs. Munitorum Storm Troopers are - as per Codex fluff - just a single regiment of up to 20k soldiers, and I would think they are nearly always busy doing some high profile mission in one of the Imperium's most critical warzones.

Inquisition Storm Troopers on the other hand are recruited in the Schola as well, and field identical armour and equipment (just with a black-red colour scheme). Their primary purpose is to act as guards on important Inquisition facilities or Black Ships, and occasionally accompany individual Inquisitors into the action to act as an elite strike team that is, I would assume, somewhat easier to acquire than a bunch of Marines or Sisters. We never got any numbers for the ISTs, but I think there could actually be more of these guys around than Munitorum Storm Troopers. If only because they tend to live longer, what with being put on guard duty rather than dropping into hot LZs all the time like their Imperial Guard counterpart.

I think most info about ISTs was in the 3E Witch Hunter Codex, although they have been mentioned here and there in other sources as well, if only in passing.

Here's a scan from the Codex Apocalypse - note the first row of troops:

Sounds ok to me. Just as long as there is a compelling reason for them to go rogue (seen daemons, for example) then it's all good.

would seeing an eldar avatar put them on the inq hit list?

So its the 40k version of the plot of the A Team?

Elite squad goes on secret/illegal mission. Person who authorized it dies, they are now viewed as criminals/rogues.

They then escape from maximum security stockade, and serve as soldiers of fortune in the LA underground, if you can find them.

naaaaah of course not...... they would be executed on the spot so no Breakouts for them... they have to run and hide a lot on the fringes of society meeting new and even more people on the fringe of society while constantly running from authorities... so its basically a han solo thing

Depends on which Inquisitor you're dealing with. The Inquisition isn't a monolithic institution, plenty of Inquisitors would find another use for said Stormtroopers instead of having them shot on the spot, regardless of what the 'rules' supposedly say. General guidelines are probably that a more Puritan Inquisitor would execute them for any risk of Chaos taint, a more Renegade Inquisitor would keep them around; more moderate people like the Almathians are more of a toss-up.

AnomanderRake wrote:General guidelines are probably that a more Puritan Inquisitor would execute them for any risk of Chaos taint [...]

I'd say this applies only if the Inquisitor they were with was considered to be involved in some pretty dodgy stuff. Radical Inquisitors get away with a lot of things due to their status, but as soon as the Inquisitor is dead, his forces are no longer shielded from retribution.

That being said, even most Radicals have other Radicals as friends and allies. Inquisitors tend to network a lot, keeping contact with their former mentor and any proteges they may have. All of these are people that might look into absorbing their dead friend's assets - be them precious artifacts, knowledge, or troops. At least that's how I see it.