Tom refers to the relationship between Daisy and Gatsby as intermarriage because of who they are. That is to say, Daisy is not just from wealth, it is who she is? Remember that line from the book about her voice sounding like money? That's Daisy. Gatsby, by contrast, is self-made. He's from another class, and for a rich man like Tom, the economic classes are as distinct in his mind as the biological races he's so concerned about.
Tom refers to the liason between his wife, Daisy, and Gatsby in terms of intermarriage because he realizes that there are feelings between the two of them. Daisy had met Gatsby well before she and Tom were married, and the meeting of the two again set off all those emotions once again. In some ways, Tom feels as though he is sharing her, or at least competing for her. For instance:
She walked close to Gatsby, touching his coast with her hand. Jordan and Tom and I got into the front seat of Gatsby's car, Tom pushed the unfamiliar gears tentatively, and we shot off into the oppressie heat, leaving them out of sight behind. "Did you see that?" demanded Tom. He looked at me keenly, realizing that Jordan and I must have known all along. (Chapter VII)
It is clear to Tom from instances such as these in the book that Daisy still cares for Gatsby. The only way to ensure that he keeps his wife instead of Gatsby sweeping her off her feet and riding into the sunset with her is to make him seem dirty to Daisy. Gatsby's business dealings are not completely legal, and once Daisy understands this, she decides never to leave Tom.