Yeah I was pretty heartbroken when I read the news on SRO. It was being made by fans of the tabletop game, who wanted to keep it as much in line with the established story as possible.
MS does own FASA intereactive, and has the publishing rights for all media for Shadowrun, Battletech, Crimson Skies (and whatever other video games FASA interactive did).
What old school Shadowrun fans are upset about is that MS has taken the Shadowrun name and some of the precepts (man meets magic/machine) and created a different world so to speak. It takes place at least twenty years before the first Shadowrun RPG, as well as throwing out much of the established lore.
I think FanPro/Wizkids have already come out and said the FPS is an "alternate" world to Shadowrun, and will not affect thier own Shadowrun games, which are a continuation of the Original story.
Sad news but the Devs who were making SRO online, Sixth World Games have decided to create another Cyberpunk RPG or MMO using a more Gibson model, no magic, just cyberpunk.
We will have to see.