In such professions like Inquisitor you just can't be unaffected by it. It would be great to have opportunity to choose between loyalty to the Emperor or to Gods of the Chaos.
That sounds like the developers would have to make an entire new game within a game. I love the idea of being Chaos, but I don't see it happening. Maybe in pvp mode or something, but I doubt we'll see a story line with Chaos as main.
Pity to admit it but you probably right. I just waiting so long RPG game in WarhUniv, you know with dialogs and choices and so on)
Yes actually, you can become a radical inquisitor. However, more strictly to your question and a truer response; no, this game as currently planned is fighting Chaos and Xenos, not joining them. However, maybe later expansions who know.