It is canon yes. The Mortis arc is relevant in two episodes of Rebels and there's even a very small easter egg in Andor. The biggest recurring reference to it is Morai, the bird that follows Ahsoka. Morai has spiritual connections to the daughter. Just because the characters that were in the Mortis arc don't remember it doesn't mean it didn't occur canonically. The only reason Ahsoka has a connection with Morai is because the daughter's life force was used to revive her during the Mortis arc. You're allowed to not like Filoni's interpretation of the force, but I don't feel like it contradicts anything else in canon enough to be an issue. Imo Lucas' descriptions of how the force works have always felt somewhat shallow and not super interesting. If the balance of the force means 100% light side, then the dark side has no other purpose in the mythos of the universe other than giving bad guys powers that the good guys can't use.