Why should the States have the rights to prevent the exercise of a citizens civil rights granted by the US Constitution?
The Constitiution, and the Bill of Rights explicitly, exists because there are things that are just not left up to 'the majority' to come to a democratic decision over. They are rights that were recognized to be inalienable rights. Time and again, courts have had to step in to once again assert that these rights already belong to all citizens because the States have used the democratic process to trample and curtail them even though the highest law of the land already should have put such questions to rest.
The Courts ruling says this. "the Equal Protection Clause, like the Due Process Clause, prohibits this unjustified infringement of the fundamental right to marry." Their dicision is not based on new law, it is simply stating that the US Constitution already recognized these rights.
Letting the States decide is letting the States pick and choose what parts of the Constitution they feel like following.