The allegiance of the Alpha Legion in the 41st millennium is not really in question. They have been featured in four Chaos Codices for a reason. They promote Chaos cults throughout the Imperium, and have been the antagonists in a few video games.
Edit: What the HH novels changed was how they got to turn to the dark side, and perhaps make some peple wonder if they really were intending to betray the Emperor and mankind. But the novels do not mean that the Alpha Legion spreading chaos cults and raiding human worlds suddenly has some kind of noble motive.
It IS in question. I question it... therefore, it is in question.
Seriously though... in all honesty they are changing the history as we speak. To make claims based on anything previous to the Horus novels would be an error in my opinion, unless you choose to ignore the modernized version of the story.
You also mention a point that cannot be ignored.
The Alpha Legion are Chaos Marines through and through, even if like the Night Lords or the Iron Warriors they pursue their own goals instead of worshiping the dark gods directly.
The allegiance isn't quite what I'm questioning as much as "are they Chaos?" Of the Legions you just mentioned, I -sort- of feel the same way about Iron Warriors which I played for over 10 years, and read anything I could get my Obliteratin', lovin' hands on.
Alpha Legion, even in old school terms never really hung out with their Brothers in the Warp. They choose to stay out of the purple eye of goofiness. There's also evidence in pre-heresy (Legion) that they always DID use local resources, and assets, and certain 'talents' that were considered.... non-standard. What's to say that the incredibly resourceful Alpha Legion are not simply leveraging an easy to use resource in 'cultists' and the like to serve their needs?
Don't get me wrong, I'm not saying Alpha Legion are 'good'. There is also hints that the legion becomes divided. How far do they go with chaos? Where and when does this split occur? I could not prove Alpha to be PURE Chaos any easier than I could prove them to be PURE Imperium. In fact, I will say I am open to the idea that there is an _in between_ . Or an area they decided to reside in that uses the 'features' of Chaos, but isn't really on the side of chaos. However, they could be serving their own agenda with no real 'side'.
So this is why I stumbled on the army. Can I use daemons? Would they be real Alpha? Are they truly using gifts of Chaos? It's too bad they aren't properly represented anymore, because in 3.5, Alpha Legion was FUN! And full of flavour. Now you have to go through the motions, and make the rest up. I didn't really care for that.