I'm sympathetic to hobbyists and SMIL enthusiasts who are losing out here, but removing SMIL isn't changing what common sites can deploy to users today.
As it's going to be removed soon, we would have to wait until Web Animations are finalized and properly implemented everywhere. Frankly, figuring out all the details of both specs and implementation deficiencies in browsers for SMIL wasn't the nicest experience (WebKit/Gecko/Blink), however there was a way to get it working in all of them in a single manner, and get 1:1 quality comparing to Flash animation. How long would it take for Web Animations to get there? As someone who was a member of a committee for an unrelated automotive standard as well as working with committee members of an enterprise messaging standard, I know very well how easily given various political interests this could turn into a solution nobody really wanted.
SMIL and IE have a complicated history. On a vast majority of recent mobile devices SMIL is perfectly usable (until Google drops the axe) and there was a surge of interest wrt SMIL driven by the availability of retina/HiDPI (small-form) displays and the need to scale animations properly, and we have an indication that our tool supporting SMIL was causing some waves in the industry as well.
I am also not sure why you'd assume only hobbyists and enthusiasts care about SMIL. I personally was dragged into it by the fact nothing else was anywhere near it functionality wise and it had to be implemented, while I could imagine much better standards myself. It was a completely pragmatic, non-enthusiastic reasoning.
That leaves us with it just not being supported by Internet Explorer.
There is clearly more than just that driving this decision, because Chrome pushes ahead with plenty of things that IE is publicly opposed to. In fact, wasn't that Chrome's original reason for existing? To implement the web platform that Microsoft was unwilling to.