I'm betting that Marvel will BS some way to not have Mystique leave Earth after SW ends, like her legendary plot-armor/shapeshifting allowing her to create a complete immunity to Terrigen poisoning. If this happens, I personally hope that this means she gets to go back to being a full-time Captain/Ms. Marvel villain (like she originally started as) now that the mutant quagmire is all-but-removed.
And just to drive it home, nobody calls her "mutant" anymore unless they want a bullet in their brain. She's just Mystique, period.