Let me try and be more specific.
When I refer to stories, I am mainly thinking of three (because these happen to be the ones I'm familiar with, though there are plenty more): I Dream of Jeannie, Get Smart, and Jane Eyre. Maybe Jane Eyre should be kept separate: the issue there isn't completely the marriage, it's whether or not Jane should have accepted Rochester, which is slightly separate from accepting the idea of marriage. But with the two TV shows, the issue was that it was acceptable for the characters to love each other and to flirt, but the dynamics were ruined once they got married. A TV show has to worry about dynamics in a different way than a book does.
The marriage in Get Smart I think was handled pretty well overall. The wedding episode is certainly better than I Dream of Jeannie's, and I think they managed to keep most of the character dynamics intact even though the marriage happened much sooner in GS than in IDOJ. That wedding speaks for it all: it's a hilarious scene in the spirit of the show, with the fighting taking place during breaks while walking down the aisle. That's kind of how it all went from there: domesticity during the breaks from the spy job--it stayed funny. And Max and 99 didn't really act very different toward each other after the wedding than they did before; they just live in the same apartment.
I think people get more heated complaining about IDOJ's marriage: they say it ruined the show because, after all, it did happen in the show's fifth and last season. But as I understand it, the show was already on shaky ground during season three, so was it really going to go longer than five seasons, anyway? And then when you look at it in hindsight (as I have done since I only started watching the show 45 years after it first aired), it's in fact rather satisfying to know that all the journeys that these characters went on ended in a marriage. Sure, a couple of the episodes after they got married weren't very good, but so were a couple of episodes before they got married.
Think of it this way. IDOJ was very much a fantasy. But sometimes for a fantasy to come full circle, there has to be a stable point at the end. It's like a Shakespeare play, where everyone runs around all crazy in the middle but the play ends with a wedding (or two or ten). It's a formula that only recently has been breaking: movies used to show a clip of a wedding at the end (whenever there was a love story, that is) and now they don't. It isn't considered necessary anymore for two characters to get married in order to solidify the fact that they have fallen in love.
But what's wrong if they do get married?
Get Smart mostly maintained the character/show dynamics, I Dream of Jeannie's wedding took place at the end of its run, and I can provide a nice and long explanation of why I'm okay with the marriage in Jane Eyre (in terms of character). So instead of ruining each story, I think these marriages helped complete them.