The thing with Harry & Linnis is that, from the show's point of view ... it never happened. Alternate Realities and whatnot are the same thing as those shows where, at the end, "it was just a dream." And hell, if George Lucas could have Luke & Leia making out without Parent organisations lynching and nailing him to a tree, then surely, Harry & Linnis - who aren't even related - can get married and have a kid with no problem.
Had Harry noticed Linnis, as we saw her, and found her attractive and was deeply hurt and angry at himself for that, and had this sort of test his character, so to speak, as a result ... it may have just squeaked by as a story element. Forcing him to accept and acknowledge the true extent of his loneliness and to come to terms with it in a way that maybe helped him overcome it. But ... we got what we got, instead, to where we, as an audience, can wonder about things like, "how did Linnis give birth to Harry's son"?
But Harry's being married to Linnis had nothing to do with anything except to include him in the story. If Linnis was married to Ensign Johnny Smith, whom we've never met, then where's Harry in BEFORE & AFTER? Nowhere to be found. But they committed to telling the story this way, so in that sense, they forced their own hand. It doesn't make it the right decision, but it's what happened ...