As you say, Wanda's powers derive from the Mind Stone. In the MCU, she and Pietro were experimented on by Strucker using Loki's staff, which ultimately turned out to be a housing for the Mind Stone. This was established in the post-credits scene for The Winter Soldier, and possibly in some dialog at the beginning of Age of Ultron.
As Thanos approaches Wanda, he attempts to use the gauntlet as a shield, while at the same time using the Space Stone to bend space, attempting to divert her powers. You can see her power and the aura of the Space Stone basically sliding over one another. The Space Stone should be able to easily divert the beam or even pop her to the moon with barely a second thought, but in this case it seems to be struggling to fight against her.
I suspect the reason for this is that in the MCU, the power of the stones can't be used against one another directly. Thanos can't use the gauntlet against Wanda directly because the stones view her as an extension of the Mind Stone. Wanda, on the other hand, can use her power against Thanos because he's just a dude with a gauntlet.
Consider the previous scene on Titan. Thanos says to Dr Strange, referring to the Time Stone
You're full of tricks wizard, but you never once used your greatest weapon.
That may be because Strange, having looked into the future, knew the dangers or difficulties of wielding the power of the stones against each other.
On the other hand, it's also worth noting that in the comics, Wanda is far, far more powerful than the typical usage of her powers would suggest. She had the ability to essentially re-write reality, at one point altering the entire Earth into a place where mutants were the ruling class, with normal humans as an underclass, essentially re-writing the prior half century or more of history.