Well, a few points...
First of all I just want to say I find it hilarious that the legion fluff keeps us discussing their intentions to this degree. It's very fluffy!

And after that I have a few points to make. First of all, since the heresy started, even in the books, the Alpha Legion was never pro-imperial. Neither of the choices they got in "Legion" was pro-imperial(either destroy the imperium immediately and defeat chaos, or save the imperium and watch it's slow but inevitable decline and destruction(though they chose a third "hidden" path)). In Deliverance Lost they operated against a loyalist faction, ending up with them not leaving all the information they had to their allies. Though this doesn't mean they were pro-imperial in any way. They had still prevented the rebuild of Raven Guard strength and the loyalist usage of the geneseed data. In the Serpent Beneath they were operating against themselves, neither Alpharius(bombing planets, grand schemes against the white scars) or Omegon(plotting stuff in the shadows, stealthing around and infiltrating anything) was doing anything for the good of the imperium. They knew this was coming before anyone else did basically, and they adapt to service themselves...
Weather the legion is divided is a mystery as well, but a fact is that Omegon is lying to Alpharius, and most likely the other way around too.
Eskrandor...yeah, we don't even know that the battle took place!

The Inquisitor with the most knowledge about the darn thing disappeared mysteriously, while there were "accusations" that he was working with Alpha Legion...mysterious and suspicious indeed...and furthermore, the Ultramarines doesn't have records of such a defeat...
Though I wholly and fully agree on the fact that we need a full Alpha Legion book more! Hopefully with a successful extraction this time...