Who said Tom's marriage was bad? Where is proof of that? We barely see her in The Godfather, and they are affectionate when they are shown. I don't recall seeing her at all in GF2 and by GF3, he's dead.

And Sonny's wife was mostly accepting. Look at other mob movies - it was acceptable behavior for a man in Sonny's position to have a mistress. As a matter of fact, Vito was the exception in that respect. Sonny's wife doesn't seem terribly unhappy, and in the scene at their house when Vito is shot, they seem very loving toward one another.

As for Johnny, Michael and Fredo, I don't think that FFC had them all married to non-Italians by accident. It was to prove that mixing those two worlds didn't work.