Loving does not apply here, as to apply it one most show that there is both "invidious" discrimination at play (which there isn't) and that the discrimination is an attempt to make a particular class superior (again, which is not the case here):
http://www.debatepolitics.com/us-constitution/215175-scotus-moderate-decision-ssm-3.html#post1064246320.
And the issue about prisoners being allowed to marry in no way recognized a federal constitutional right to marry, but that the state had no federal grounds to deny either rights or privileges to prisoners that were not specifically denied in the constitution or denial of which constituted cruel and unusual punishment. Rights or privileges not explicitly granted in the constitution are left to the states and the people. Marriage is one of these.
But, even if marriage was eventually declared a federal constitutional right by some convoluted erroneous reasoning, it's still "marriage", meaning "between a man and a woman as husband and wife". By it's very nature, "marriage" rightly discriminates between a single person by him or her self, three or more people, a man and a little girl, a dog and a cat, .. and a man and a man and a woman and a woman.
No exceptions can rightly be made with respect to the word "marriage".
If you want to have private enterprise and government recognition of certain specific domestic partnerships (marriage itself is a civil union domestic partnership legal statute in every state), then each distinct civil union domestic partnership must be defined in detail and identified with an identifying word .. so "homarriage" or the like would be a new civil union domestic partnership "between two same sex people as husband and husband or wife and wife" or whatever.
But that's rightly up to each state to decide, as there is no federal constitutional even remotely applicable passage in this matter to force states to create specific statutes.
Justice Thomas is absolutely correct, in that not only is it apparent that the SCOTUS is tipping their hand that the majority will attempt to construe a federal right to the ridiculous oxymoronic "gay marriage" / "same-sex marriage", but that that would obviously be the wrong decision, as though clearly the majority of Americans favor recognition, the majority of Americans also don't support that recognition under the inapplicable term "marriage", and because the SCOTUS simply has no final conclusion as to whether gay is from birth or a conscious choice, they cannot intelligently conclude it's an inalienable right.
The SCOTUS simply has no rationally intelligent grounds to conclude that "any two people" can "marry", both with respect to definitive propriety, respecting words and their true meaning, constitutionally, and with respect to the majority of Americans who have yet to show that gays marrying is a time-honored cultural reasonable and customary tradition.
Ultimately, the likely thing the SCOTUS is going to do is to require same-sex union recognition in every state but to let each state decide what to call that particular union. Some states will call it rightly "homarriage", and others will erroneously refer to it as "marriage".
But the right thing for the SCOTUS to do is to allow recognition in every state but require that it be given a name other than marriage, as it's reasonable and customary for adult humans to bond one-to-one (not polygamously), but there is no reasonable and customary cultural tradition to call such bondings "marriage".
Again, marriage is a contract, and contract law is the province of the state, not the federal.