"Now, what explanation other than magic do you have for bolts of lightning and thunder?"
"Now, what explanation other than God do you have for the sun rising every day?"
Just because you can't explain it doesn't mean it's magic. That's why I am asking you, has it ever been stated anywhere what MCU Scarlet Witches powers are? For all you know the Gems are incredibly sophisticated devices. Do Marvel comics distinguish between magic and other forms of Superpowers like DC? Superman does supernatural things, but isn't magic, neither is Green Lantern. We have clear examples of devices in the MCU that look like magic, but aren't. The Bifrost, for example. Asgardian tech, in general. If we glance over to the X-men, you have lots of people who can do all sorts of crazy stuff and aren't magic.
Comic books tend to be unnecessarily specific when it comes to the origins of powers. Just because two characters seem to be doing the same thing doesn't mean their powers are the same. If Agnes is more powerful than Wanda, what does she need her for? I'm assuming she needs Wandas power to accomplish something. Maybe she's trying to put Mephisto's Soul into Visions body, but needs both magic and the powers of the infinity gems for that.