I'm going to look at this positively, because I'm not a cynical conspiracy theorist.
This seems like a pretty good deal to me for both parties involved, as long as it doesn't tie indie developers down to anything, (EA getting sequel rights for example). Don't think its a bad thing for big game companies to break into the indie market,in fact surely it can only improve the industry, convincing big publishers to take greater risks, improving the triple A buisness. The big working with the small. This is at no risk to indie devs who don't want to take up the offer either, devs who used kickstarter funds to avoid the "corporate machine" take this offer up, and others who used kickstarter purely because they had no other method for gathering funds have this option, which means they can put the money they save through this to good use elsewhere. So Notch has no reason to get on his high horse over this.
Also, this will greatly help improve origin. Origin can seriously do with some indie titles, the system is in desperate need for some more variety. I very rarely use it, only got it for SWTOR, and have only brought Gatling gears and warp through the system (a week before the EA indie bundle came out on steam -_-). More indie games at competitive prices would help sway me to using the thing more, perhaps they can allocate indie games their own tab on origin, and give them some front page advertisement.