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Hello.

My gaming group for Rogue Trader is, to say the least, a rather odd bunch - our neutral good Rogue Trader wants to escape the Imperium, our chaotic evil cleric is dedicated to Nurgle, and our chaotic good tech-priest is fascinated by xenotech.
As such, I'd say that my group is fairly liberal minded.
Given that we are ploughing unexplored space currently, and given our captain's dissatisfaction with the Imperium, I quickly saw the opportunity to have an adventure involving my favorite and first Space Marine Chapter, the Soul Drinkers.
For those of you unfamiliar with this Space Marine Chapter, here is a thorough and comprehensive biography: http://1d4chan.org/wiki/Soul_Drinkers

For those of you familiar with Sarpedon and his eggplants, you are aware of the chapter's idealogy: Protect the common people, avoid the shackles of the Imperium, and fight the good fight for the survival of humanity rather than religion or profit, line up with the viewpoints of our Rogue Trader and tech-priest (even if it doesn't seem like it, trust me - our parties would get along quite well, save for the obvious Nurglitch cleric in the midst).

What concerns me more is the idea of using a Chapter whose history is already set in stone - we who have read Phalanx know exactly where they're going. However, the Soul Drinkers often mention adventures and battles that take place in between the books - the way I see it, there are two possibilities.

A) The Soul Drinkers that I use in Rogue Trader consist of the main chapter (Sarpedon, Lygris, the Brokenback, etc.) in between the events of Chapter War and Hellforged.
B) Instead, the Soul Drinkers I use in the game are the various novitiates and scouts that left the Chapter at the end of the second Chapter War, those who followed Eumenes and felt that the Imperium should be toppled.

What do you think? Is this strange, a good idea, or a bad idea, and which option seems more natural?

Seems like your group has a more dnd mindset to this game than rogue trader. RT characters don't really have alignments. Also, i assume your cleric is a missionary, but taking in a devoted priest of nurgle isn't really a "We don't approve of his religion, but he does make himself useful" kinda situation. Chaos worshipers are evil, no exceptions, and that's just the truth, not imperial propoganda. It's one thing to trade with chaos priests for guns and such, it's entirely different to have one of them on your bridge crew as one of your closest allies and advisors. It also seems your crew won't remain rogue traders for very long and quickly get their warrent annuled and become renegades. I'm curious as to how familiar your players are with the setting.. But hey, who am i to tell you how to play?

To answer yoour actual question, I wouldn't worry to much about being strictly by-the-books-canon about how you implement the soul drinkers. After all, if your players didn't raise an eyebrow at being mates with a nurgle-devotee, i doubt they'll crucify you if your soul drinkers aren't following the right ideals for their time period. If it's more of you personally want to implement them correctly canon-wise, i'd tell you to go with which one better serves your particular, individual campaign. Don't choose one that you enjoy less for your adventures because it works better canon-wise. If the party wants to ally with the soul drinkers in toppeling the imperium, i'd go with b. But really, just build your campaign the way you want it, and go with the option that better fits what you came up with.

My players are extremely familiar with the setting, but they have no qualms about working with the corrupt - some of them actively want to align to Chaos, and others just want to avoid earning corruption themselves but are still willing to tolerate his presence - their attitude is, as you said, "We don't approve of his religion, but he makes himself useful". However, I must stress - we are not Imperial. I absolutely agree - if we are ever contacted by the Inquisitorial authorities, we would probably be executed. We are already renegades, essentially, delving into unexplored space to avoid the eye of the Imperium and the Inquisition. So yes, technically we are no longer Imperial Rouge Traders by any regard - but that doesn't mean we don't have the same drive to explore or profit.

I imagine I'm probably doing to go with option B - our party's leader, Rouge Trader Venini Belarus, is known for harboring a special hatred of the Imperium. I imagine that Eumenes's former men would fit right in, and it allows me to avoid the party becoming too overpowered by only allowing a few marines to be used in very specific situations, as opposed to having a whole chapter on their side.

Whatever floats your boat. If everyone is having fun, then go for it. I pray that the inquisition spares you with only a mildly excruciating death.

I like the Eumenes idea

You could have many interesting scenarios arise if imperial agents do come after them, if they want to align with Chaos, let them, then send the inquisition after them and see where they run.