LIke everything - it's complex
Having lead an IT department for an Australian Heart Research organisation, I was there during our (all Australian MRIs) negotiations with MS.
Couple of points: Some "NFP" have positions such as 'GM of Commercialisation" and other NFPs include organisations such as football organisations (the AFL; NRL etc.) - so not all NFPs are equal.
The call to cut the NFP pricing was made years ago & it has been ongoing in MS (especially as the person at MS who made the call has left). It has improved from version 1, which was there is no NFP at all.
Another problem is a lot of medical research in the US has HUGE $$ behind them, unlike in Australia, where our scientists often rely on government funding, yet there is only an 11% success rate in submissions - so this change could have really hurt some places.
Pushing NFPs to the cloud is a very good thing. Most are already there, but those who are not, generally, have pretty average IT security/Backup/DR capabilities. It also forces their organisation to invest in IT.
So, it's a bit sh%t and there will be a transition cost for some, but in the long run, the NFPs will be in a better place.