A note on the Space Marines and "spiritual purity"; Many Space Marine chapters does not venerate the Emperor in accordance to the Imperial Creed. They consider him an amazing individual, the epitome of humanity, their Emperor and commander, but it's important to note that they don't buy into the Ecclesiarchy's (and by extension, the Inquisition's) view that he is in fact a god. Many only begrudgingly accept it and have compromised by enforcing the presence of Chaplains in their ranks, which do preach the Imperial Creed.
The motivations of Chaos is as varied as it's worshipers. Chaos itself and, to my understanding almost all beings of the Immaterium (the warp) essentially feed of any and all emotions. There are "good" aspects of chaos that unfortunately have taken the backseat in almost all modern 40k fluff - for example, Slaanesh is the god of excess, not just pleasure - anyone inclined towards excess, such as a banker that REALLY loves his money, or a painter that is completely submerged in the execution of his profession, could be a potential worshiper of Slaanesh. Similarly, Nurgle is the god of despair, but also permanence - anyone afraid of change, such as the fear of death, is a potential worshiper.
It is also worthy of note that the actual Major Chaos Gods are not the only 'gods' of the warp. Furthermore, they are incredibly disinterested in the affairs of mortals. They are interested in gaining the upper hand against their brothers, more than anything. Chaos is rarely a unified force and the major gods of chaos will almost never take a direct interest in any of the on-goings of the Materium; such things is the affairs of lesser demons. Remember that even certain greater demons or demon princes are exceedingly rare to leave the Immaterium - there are several of the old Primarchs that were corrupted during the Horus Heresy that haven't left the Eye of Terror for 10,000 years or more.
As for the question on rogue Marine Chapters, there's no such thing as an "independant" Chaos Space Marine chapter; By their very definition, they are influenced by the powers of the warp and at the very least, controlled-via-proxy by chaos entities, greater demons or chaos gods. There are however several 'regular' rogue Space Marine chapters that for a number of reasons have been excommunicated. This can be for any range of reasons - they may have been affected by Chaos, but not to the extent that they have lost their minds or souls. There may be mutations in their geneseed that have become unacceptable by the Inquisition. They may simply have been at the wrong place at the wrong time. A misunderstanding may have caused them to be embroiled in a conflict with other Imperium forces.
Regardless of the reason, yes, there are rogue Space Marine chapters that are still loyal to the Imperium. I think there's even one that took it upon themselves as penance and have been lost for thousands of years.
There's also many chapters that are very close to excommunication, but the Inquisition can't actually do it because they're simply too big or too strong. The Black Templars have completely disregarded the Codex Astartes and the reduction of Space Marine Legions into Chapters - at this point, the Inquisition have contemplated excommunication, but they are fanatically loyal to the Emperor and frankly, they're not sure that they could take them. The Blood Angels & Space Wolves are also good examples of chapters that are very close to excommunication but they are simply in such positions so that, even if the Inquisition wanted, the Space Marines would stick together, refusing.
It's also important to remember that even though the Inquisition basically have a carta blanche when it comes to giving orders around most of the Imperium. But when it comes to the Space Marines, they can only ask. This even applies to chapters inexorably linked to the Inquisition, such as the Deathwatch of Ordo Xenos, or the Grey Knights of Ordo Malleus. Inquisitors can't actually order them to do anything. No-one can. All orders to the Grey Knights must be carefully worded as "requests".
And wow, yeah, sorry, I really went off writing there. Sorry.
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