My guess is that they pulled the pdf versions of older adventures because they were not making enough money on them and because they want to hurt Paizo. With Pathfinder they might think that Paizo has become a competitor for them. I mean, they gave the industry the OGL and now Paizo has the right to continue this line, turn it into their own, publish core rulebooks (which will sell decently, I guess) and take hold of those who WotC wanted to convince to play 4e to begin with. That is why I believe Paizo was likely not to go go with 4e with any license that was more strict than the OGL. As Eric Mona said in one of the more recent Green Ronin interviews: Why should the company have to rely on the goodwill of another company (WotC) if they can publish material based on the OGL, over which they have full control, 8+ years of design experience and an already existing fan base?
So, Paizo is a competitor of WotC now, as 3.5 seems to be a competitor of 4e. And since it is easy to transfer old modules into 3.5 (again, with 8+ years of experience with the 3.5 system), pulling old modules probably hurts Paizo, because old modules support their product, not WotCs 4e.
My guess is that WotC will eventually publish old modules with the 4e rules for cheap and find a different way to sell digital content through DDI. And a lot of people will be ticked. And I will not understand why.