Agreed that the state's rights rhetoric is applicable for certain things, but not for a nationwide issue of equality. Rubio should have said something to the effect of, "my personal beliefs will in no way shape or form discriminate against having equal protection under the federal law for ALL American citizens." In fact, I think all conservatives can and should get behind that even if they oppose it on a personal level.
How do you want Rubio to do that? It isn't as if congress can pass a bill declaring homosexual marriage legal. If you want "nationwide equality" or whatever, your either going to have to wait for the SC to somehow declare it a constitutional right, or pass a constitutional amendment.