Does the motive matter? What matters is the written law and what the written law accomplishes, not the motivation for the written law. The motivation for the law isn't law. The text of the law is the law, the text of the law regulates behavior, creates privileges, and has results, effects, but not the motivation for the law. The fact is section 3 of DOMA was written for federal tax laws and regulations and not for any state laws, state taxes, or state regulations. Relying upon the motivation for the law is a very poor reason to rule against a law. The motivation for the law has no effect but the law itself has results and it is the law itself which is paramount, not the motivations for passage of the law.
The law itself does not interfere with any state power, none, and the motivation for the law does not change this fact. DOMA section 3 defined the meaning of marriage for federal law and only for federal law, leaving the states complete and absolute discretion to define marriage under state law.