I don't see how it's a stifling of States rights, if anything it should have been incorporated from the beginning to strengthen them.
People mean different things when they use the term "state's rights." As you are using it, yes, your premise is correct. But there are those in our society who want to use the states as their platform for continued bigotry and laws which illegally infringe upon the rights of others.
It is those kind of "state's rights" that are (and should be) stifled by the Incorporation Doctrine.
I've seen a few (but only a few, to be fair) posters in this forum come right out and say they don't mind if the State infringes on their rights, since if they don't like it they can just move to another State. Without the 14th you could leave the State but the State could use just about any means to pursue you, for any reason, as long as it was done in a manner consistent with FF&C. And its sister states would be forced to comply and enforce those rulings, regardless of whether it violated their own laws. Anti-14th folks think about that concept for a second then tell me establishing minimum standards of fair play within, between and among all States is such a bad idea.
Section 1 of the 14th should have been in place from the inception to ensure the rights of States to be free not from Federal interference in the areas where they hold sovereignty, but from infringement on that sovereignty and on the basic rights of their own citizens by other States.