My story is set on a continent where racism is rife, and the people of that continent are trying to force out all of the people who moved there from the southern continent, and their mixed-race kids. My MC is mixed race, but no-one on the continent knows this. She much prefers the lifestyle of the northern continent and hates the way the southerners are changing it. Because of this, she hides her racial identity and becomes a driving force for getting rid of the southerners. Do you think this is a good enough motivation for someone to cause such suffering to people whose racial identity is half her own? It's not that she wants to cause suffering to those of southern descent, she just wants them to go back to their own land, so that the northern land can stay the way she likes it.
In short: Yes. Very much so, I might add this is a powerful driving force for many people to fight injustice in general. Get out... stay out... and don't come back... sounds like a fair motive. This is our land ideals like that. Works. No plot problems to speak of that I can see. Go for it.
Yup... Oh yah, no questions asked. if you want to add in some "Internal strife" you can, but in most cases when this happens people disown their perceived "Evil heritage" Hope this helps.
It's one of the saddest things about humanity is how easily we can turn on people just like us. History is riddled with examples of this, if not built entirely out of it.
I don't think there should be any sort of problem with your plot, although as mentionned above you could add in some sort of internal debate which could be quite interesting.