I don't really see how the comics affect those other merchandising ventures, though. Other media besides the comics are what merchandise usually comes from. Look at most of the toys or lunchboxes or whatever from the past ten years and what are you likely to see? The movie Spider-Man or Spectacular Spider-Man's Spider-Man. Look at the stuff from the decade before that and it's the '90s animated version. What goes on in the comics doesn't really help or hinder what goes on in other media because comic readers comprise such a miniscule part of the fanbase. In all three of those other media ventures I mentioned, Spider-Man was portrayed as younger and single, even though he was married and pushing 30 in the comics at the time. Right now we've got Ultimate Spider-Man in development which, once again, will feature a young, single Peter Parker. I don't claim to know a lot about the inner workings of Marvel as a business, but it certainly seems to me that a married Peter in the comics doesn't really make a whole lot of difference to the image of Spider-Man in other media and merchandising.
Marvel had at least one car ad on their back cover that featured Spider-Man webbing up Doc Ock on the top panel and doing food shopping as Peter Parker with a familiar looking red-headed woman in the bottom one, with art by Todd Nauck. The premise of the ad was that their car was good for both fun and responsibility. Car manufacturers are hardly shy about using married couples or families to sell cars, especially SUV's or larger cars.
So at the very least, there are some merchandising arms that still seem committed to the idea that Peter and MJ are married or "co-habitating".
Of course, one might argue that a Spider-Man who can be all things to all people - devoted married man or swinging bachelor - in terms of advertisements isn't such a bad thing for the bottom line.
Your point about sales of comics being the bottom line is key. If BND had been as colossal a sales failure as, say, the idea to given Daken WOLVERINE and shift Logan to WOLVERINE: WEAPON X, even Joe might have been tempted to reverse course. The fact that OMIT happened when it did was basically to provide a sales spike. To be honest, it is difficult to wage the sales of the Spider-Books pre-OMD. For at least 2 years before OMD, all three of Spidey's comics were in perpetual crossover with either themselves or CIVIL WAR. Which in itself said something. The reshuffle of the title to thrice monthly (now twice) sought to basically maintain that. Post-BND, sales on the collective ASM aren't anywhere near where they were in the 90's, but they've remained stable around 52k per weekly issue (or over 156k for the three combined; twice a month it should shift to 104k for both). Certain storylines can spike things for a month or so. BIG TIME's initial issue saw a sales spike as well. One could argue that the half million sales for "The Obama Issue" alone netted enough moolah to survive a few stumbles.
Also, it doesn't seem like any other editors or writers at Marvel are eager to turn back the clock on Spidey after over two years. It isn't like Tom Brevoort wasn't an editor at Marvel during "the married years" of ASM. Alonso was editor during JMS' entire run on the title, and JMS was the one who re-united Peter and MJ after Mackie had them split up when he departed (by sheer coincidence, Peter & MJ reconciled in time for 2002's "SPIDER-MAN" film). Dan Slott's been a regular writer on ASM since BND started, and I don't think he would have been promoted to solo if he was dead set on turning back the clock. The downside is that even 2+ years later, it is a wedge between fans and STILL a controversial topic. It could very well be Quesada's "Clone Saga".
I do wonder, though, if the X-Books will shake off the malaise they gained from M-Day at long last. While there may not be any compromise about a marriage to MJ, surely people can't be inflexible about more mutants, and about getting the central metaphor back into the franchise. I am at the point that I might have seriously considered trying Kieron Gillen's take on them, if the editorial direction right now as well as in the recent past wasn't so dire.
I noticed that too, and I thought the timing was so odd with what was going on in comics with MJ. 
