Yes. It's not racist to tell someone, "if you don't like it, leave." That's just the classic, "if X political outcome happens, I'm moving to Canada!" from the other side of the aisle.
It's not racist to tell a libertarian to move to Somalia if they like libertarianism so much. Even if the libertarian in question is black.
Even though the phrase is used by racists, it still has utility and meaning that are not racist. That meaning can be applied even in cases where the person being invited to leave is indeed a different race than the person issuing the invitation.
Telling Ilhan Omar, who is literally a Somali immigrant, to go to Somalia, fix it, and then come back and show America how it's done, is perhaps unfair, but it's not necessarily racist.
Indeed, telling an immigrant who doesn't like America to go back where they came from seems like an obvious and reasonable answer to their expressions of dislike. It might be more reasonable to invite them to work on making America better. It's been argued that Omar doesn't hate America, she just wants to make it better. That's fine. I'm not arguing against that.
Anyway, I don't see carelessly telling an immigrant, if they don't like America they can leave it, as an expression of bigotry so heinous that it must be ended at all costs. Presidents say stupid and bigoted **** all the time.
This is just yet another attempt at forcing The One Thing That Will Bring Trump Down. Let it go, man.