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So I am trying to work on some fluff and thought about if a chapter emerged from the warp in a sector that is revolting but not turning chaos. Would they perhaps believe the revolting was right? Take the calixis sector. They believe they are fighting for the emperor against those who are wrong. Could a chapter join that crusade believing perhaps there is another civil war? Any sectors beside calixis this could work?

its 40k it depends!

Questions:

Why has the Space marines traveled to this sector - own mission, call for help, misjump, travelling elsewhere
Who do they encounter - an Imperial official asking for help against rebels is likely to get an audiance if not actually help.
How large (or small) is the Space Marine force
What is the temprement of the Chapter
Do they have any previous history with either side.
Is the Inquisition involved?
Perhaps the Mechanicus is involved with onoe side or the other and the marines have history (good or bad) with them

It could certainly work if they were for instance given evidence that the Imperial authorities have fallen to Choas and perhaps some of the rebels have fought alongside them before - maybe a debt of honour is owed......

They could even just start asking questions - which maybe difficult to answer or avoid...........

Enemy space will most likely be empty. Space is really, big and empty you know.

If it wasn't empty well then you could risk an accident like this. http://www.destructoid.com/one-pilot-s-mistake-leads-to-massive-battle-in-eve-online-243509.phtml

I can't remember if it was Space Wolves or Salamanders, but they did rebel once against the Inquisition when trying to escort people off of a planet that had seen demonic forces and didn't believe they should be cleansed for it.

 Tinkrr wrote:
I can't remember if it was Space Wolves or Salamanders, but they did rebel once against the Inquisition when trying to escort people off of a planet that had seen demonic forces and didn't believe they should be cleansed for it.

Space Wolves - battle of Armegeddon

I think this was what happened to the Lamenters and Mantis Warriors, although not exactly as you described.

Namely they were tricked into thinking Huron was the "good guy" and fought alongside the traitors.

I'm thinking warp jump gone wrong. They end up on the back side of the Calais sector which is in total war with multiple planets. It looks like imperial on imperial.