I definitely hope they keep the Kree connection AND the basic origin story unchanged. I'm trying to think of a case where the origin story has dramatically changed, but really can't think of one. I guess maybe Ant Man sorta, but DS, IM, Hulk, CA are all pretty faithful retellings. Thor doesn't have an origin story really, but they did lose the "turn back into Donald Blake" stuff if he didn't have his hammer for a certain amount of time....Jane is different (tho not a SH).....let me know how that worked out for them.....
I still think Carol Danvers will appear in A3. It's a super high profile movie followed by CM and I think it's WAY too good of an opportunity to miss for hyping her movie. I say she pulls the hero move seen from the perspective of others and disappears. The actual origin will, for sure, be in CM and I hope it's Kree Kaboom. I'd love to see the opening of CM be of Carol in her fighter jet with all hell breaking loose around her, she pulls the hero move from her perspective that should kill her and "Shazam" she's Captain Marvel (ooops....wrong one...).
Keep the Kree....keep Kaboom.....if possible, keep Marv. If I had my way, he saves her post hero move. He'd be in A3, but we don't even know it until CM.