"the two "missing" legions was purged"
I dont quite understand what you mean by this, its my understanding that Omegon and Alpharius are essentially one person, one soul in two bodies. Therefore theyre the joint primarchs of the Alpha(AlphaOmega makes more sense) legion therefore he isnt the primarch of one of the purged or unnamed legions.
And the choice given, either help the heresy to destroy chaos or save the emperor to create the 40k universe we know is an awful one, but their actions seem questionable, they dont appear to do much of either considering their failure to keep the Khan or Russ in place.
Also does anyone find it weird how a legion so dependent on coercion and manipulation can appear to be played into joining the Heresy or not, which adds the whole extra level of whether they arent following the Cabals advice and instead are following their own agenda, a "third way"
All in all the book was fantastic but naturally left more questions asked then answered