Yup. But after the merger, there may be a little more stability that they no longer feel the need to store their original works in an escape pod.
If Microsoft were interested in producing further games in the Eora setting, it makes sense for them to not want to arrange licensing for it, or prevent DRIL from independently marketing Pillars-themed board games or frozen dinners or whatnot.
In some ways, it bodes well if you like Pillars of Eternity; it appears that Microsoft does too, and they have deep pockets.
Feargus has frequenstly talked about a Pillars game that looks like Skyrim. Including the IP in the aquisition makes this more likely to happen.