where the alpha legion is persuaded by the cabal to fight with Horus to ensure the destruction of chaos in the long term

and Grammaticus persuades Pius to aid 'Him' as its all going pear shaped .

is the Cabal incredibly Machiavellian and are playing both sides, or has the Cabal been working for chaos all along, and 'He' is actually Horus. Of course, the third and most likely explanation is that BL have messed up

That Grammaticus, disgruntled at their former masters, has set up Ollanius Persson in order to disrupt the Cabal's plan. The Cabal has been for a Chaos victory all along - they believe Horus will unwillingly cause the extinction of mankind, causing only minimal damage to the Galaxy. The alternative as they have foreseen it is not an Imperial victory, though but a stalemate that would drag along for millenia, ending in a conflict of cataclysmic proportions that might destroy the weave of reality itself. They believed that, by turning the Alpha Legion, they'd be tipping the balance in Horus' favor, but obviously something went terribly wrong along the way.

I thought that Grammaticus was never truly on board with the Cabal and even during the events of Legion he appeared as quite a loose canon. I expect he can't quite stomach the events he's put in motion or the idea of humanity being destroyed, and is so working to ensure a flat-out Imperial victory, as said.

Personally, I don't see the Cabal as actually working for Chaos (as in being pawns of Chaos), nor why others particularly would.