On what are you basing his inferiority? Her ability to compress Time and Reality? Malygos is a very complicated character to bring into a debate between two magical users. His ability to block magic in more than one way, shared with his ability to lock various characters out of their magical powers make him a very though opponent.
Since Malygos might has never been overriden by any other than Neltharion /w Demon Soul (Under which state Malygos was weakened, and the same time, the Demon Soul which empowered Neltharion held a portion of Malygos power), it is hard to imagine him lose against magical users at relatively earthly level. I am aware of Ultimecia's compression ability and that it is anything but earthly, but she is in an earhtly league. It's not like she's a Spectre or a Mr. Mxy.
In Warcraft, magic is not always dependant on who is stronger. Magic is of a whole different reach there. Illidan was able to ward his mind from Sargeras, while in fact Illidan is not even a match for the Titan. Sylvanas was able to silence Dar'Khan, who had the power to kill her with a flick of his finger.
Even if Ultimecia is more powerful than Malygos, it is not sufficient proof that she could resist his ability to block her access to magic. Has Ultimecia shown any type of resistance that you can use as an argument in benefit of her against the mightly silence of Malygos?