I wonder how they are going to handle Malerion, if he does exist, contrary to what this snippet claims. When the End Times came around, Malekith got a redemption arc of sorts. He became the Eternity King, got to marry Alarielle (even though that was kind of a loveless marriage), and outlawed the Cult of Khaine. I doubt he'll be too happy with Morathi bringing back the Cult.
The Cult of Khaine that's in operation now is very different to what it was in the past.
1) The Cult no longer has any Chaos influence besides the bodily mutation to Morathi and the souls saved from Slannesh's belly (which is a constant all the Aelves rescued that way suffer with). So there's no lingering taint or call to chaos. If anything the cult is almost as dedicated to the destruction of chaos as it is the worship of khaine
2) He's likely aware that Khaine isn't even getting the worship energy and that Morathi is siphoning off the power for herself. I think one of the Maligan Portents stories even suggests that he's aware of her trick into twisting of the harvesting spell so she gets more souls.
3) Whilst I don't think they love each other like mother and son (heck Morathi is insanely jealous that he's got godlike power and she has to steal power to get a demi-god powers); they are the last remains of their people in god-form and who survived the Old World. That seems to build a shaky alliance between them. You can tell its not perfect because Morathi was pushed into the darkest corner of the Realm of Shadow whilst Malarion rules almost all the rest (or at least the vast body of the central regions).
4) In the Malign Portents stories we see the two conversing cordially. So they at least get on or see mutual benefit. Considering that the other Aelf gods and Sigmar were all allied heavily against them in the Old World, chances are the pair of them see in each other an essential ally within allies. Someone who they can trust or at least understand better than the others.
He won't war or turn on her overtly, the Cult forms too useful a tool. But I'd wager he would look to ensure her position doesn't rise to challenge his own - be it by spread of the Cult and/or her own power growing. She, meanwhile is likely more than willing to find ways to subvert, control or otherwise steal Malarion's powers and influence.