Right. The judge ruled that DOMA violated the fourteenth amendment because its definition of marriage doesn't provide equal protection to homosexuals. Therefore, DOMA is an invalid law. If that is the case then any law, state or federal, which defined marriage as between a man and a woman would be be a violation of the fourteenth amendment so, this ruling, if upheld, would overturn the laws of many states.
Which, of course, is more or less what Loving v. Virginia did. The judge found that the state law violated the 14th amendment, and thereby invalidated that law and many similar ones in other states.
Meanwhile, in part of the same opinion, the judge invoked the tenth amendment to say that the federal government was not allowed to dictate to states how they define marriage.
That's right. The Federal government is not allowed to dictate to state how they define marriage. The Constitution, however, can and does dictate that certain discriminatory definitions are not acceptable.
No conflict.