To be completely honest (and giving my own opinion on this, rather than WotC's), unless you are developers and publishers a lot of this won't affect you one bit, and if it hadn't had such a stink around it most would never have even noticed any changes at all. A lot of people are looking for problems where there are none.
At no point did anyone from Wizards of the Coast confirm the rumor that the GSL would be on a company-by-company basis. At that time (and even now) the GSL was not technically complete. Scott and Linae and everyone else at WotC are all under NDA, which limits what they can say and when. Even the much (mis)quoted Scott Rouse Post doesn't confirm that they would limit a companies ability to post through the OGL, simply that they would be actively encouraging the use of the GSL amongst third party publishers and that 3pp would be free to choose between OGL and GSL, but that there would be a choice involved. At no point did any major 3PP complain about the actual GSL. Chris Pramas said that he was contacting for clarification, but if the allegations were true than Green Ronin would stick with the OGL so that it could continue to support M&M. Clark Peterson actively supported it even when he thought that it might be on a company basis (though he didn't claim to believe that particular fact).
As it is, this is about what everyone expected. I can't imagine that anyone was really planning on releasing the same exact product lines for both 4e and 3.5 anyways. Quite simply put, it wouldn't have made economic sense to split development time for a product with such a narrow audience. I can, however, see the desire for publishers to maintain at least one of their current lines in 3.5 while transitioning the others to 4e, and the GSL apparently allows this.