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Well this is highly speculative on the one hand, and on the other hand, is pretty naive for thinking that there aren't already small pockets of people fighting to preserve their culture.
I know you didn't say "culture," but I can't envision this situation without seeing a race of people fighting to preserve their culture first before any thoughts of genetics come in. This leads me to another thought: I don't think that our nature would encourage us to reproduce only out of one gene pool when it means we risk extinction.
At any rate, I think this is a silly scenario. Just look at any First Nations/Native American reserve. The powers that be have removed their means of fighting to preserve their heritage, so based on this example, I can't see a small minority reacting "more violently," since the means of their revolt have been taken from them (amongst other things).
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