Now, see, I've always had a theory about the Alpha Legion, and the theory that may or may not still be loyalists. The whole tendency for the Legionnaires to call themselves Alpharius is interesting: it means that potentially, anyone in the Legion can take command and direct things.
But it also leads to the problem that the Legion can remain a viable fighting force without anything to unify it. Everyone is Alpharius, and as of the 41st Millenium the Alpha Legion is a confused morass of factions, some Loyal, some traitor, some who knows what, and even within an Alpha Legion warband there are are a host of competing agendas. Beneath the layer of paranoia and mistrust, the only thing the modern Legionnaires have in common with each other is the name Alpharius.
In other words, my theory is that at some point the hydra grew too many heads, and have become hopelessly tangled together. I think it's plausible, at least.