I wonder about that as well, but then the rerelease also had a Grover segment replaced with another segment. Don't know what was so wrong with the Grover segment.
But would a young Maria really be a problem? Rock & Roll and Dance Along both include a very young Gina, and as far as I know those are still in print (though I haven't seen copies in stores for years, but at the very least they were still in print in 2005). There are many other old videos with the cast that are still in print, though maybe not with such obvious younger looks. Bedtime Stories and Songs is really the only video that got altered for a rerelease (well, so did Big Bird in China). While not every video release is still in print, I think everything that was released on DVD is, though I'm not too sure on whether the Old School or Play with Me Sesame releases are in print (I haven't seen new copies of any of those in years). As far as I know they never altered Sign Yourself Silly, which has the original celebrity edit of Put Down the Duckie and a Don Music segment.
Though it seems that starting in the 1990s if not earlier they pretty much stopped showing segments where the adults look younger (years before they seemingly stopped showing earlier segments with the Muppets looking different). There was an episode from season 30 which included "The Word is No", with Gina looking a lot different, but that was presented as a flashback. Interestingly, last years release of "Elmo's World: The People in Your Neighborhood", aimed at today's target audience (not nostalgiac fans), features two early versions of The People in Your Neighborhood, with younger-looking Bob and Maria. So I guess they must not be too concerned about confusing kids now (if only they'd feel this way and put the older clips in new episodes and more new video releases).