Plan of extermination is a bit hyperbolic, since the United States never had a plan of extermination. They might have had policies that had that consequence, but that's at least a noteworthy distinction.
Indian groups had an identifiable tribal structure. They were dealt with by treaty through the Bureau of Indian Affairs. For Mexicans of various ethnic origins, it would be impossible to differentiate unless they had tribal structures. It's possible they'd either create a Bureau of Mexican affairs or grant them all citizenship rights. There isn't any tenable compromise between the two. I think they'd probably pass discriminatory laws that made it easier for slave holders to enter the area, which would quite possibly overwhelm the original population, but that's a bit different. Of course, the whole thing would be impractical, which is why it was voted down in the first place.