Maybe the Kree use her as a prototype for the ultimate weapon. The Kree could take the culmination of thousands of years of work including the Inhumans project, as well as the combined work of like 12 different super soldier programs or something. They don't expect her to survive the procedure. They plan on using her DNA to create an all powerful army, but she survives, and escapes.
Nah, somehow to make her powers the result of structured experimentation somehow diminishes her essence to me.
Like flickchick said, the same broad strokes can be used with zero necessity for said magic wish fulfilling thingamabob. I would keep both her origin and the plot somewhat simple.
* There's a Kree doomsday device meant to obliterate Earth... maybe they blame Thanos' currently ongoing universal rampage on the meddling Earthlings.
* Mar-Vell's been a long standing Kree spy on Earth who was previously unflinchingly loyal to the Kree empire, but not completely unsympathetic towards humanity.
* His (not necessarily romantic, as flickchick said) relationship with Carol causes him to reevaluate his loyalties.
* Mar-Vell makes a split second decision to save Carol and, by proxy, humanity. They disable the "doomsday" part of the doomsday device, but it still explodes sending cosmicish radiation. Mar-Vell shields Carol. Mar-Vell DNA + radiation + Carol's Earthling DNA causes a freak accident giving Danvers her powers.
* Mar-Vell's branded a traitor by Supreme Intelligence thingy.
* Mar-Vell comes clean to Carol. He's pretty badly wounded though, so he's out of commission for a while. He says he'll heal in time, but implores Carol not to turn him in. She acquiesces.
* Glorious montage of a conflicted and somewhat emotionally wounded Carol exploring her Cap'n Marvel powers. Kinda bittersweet stuff here. Yes, Mar-Vell betrayed her to an extent. But raw power. And FLIGHT!
* Kree attack Earth. They send a small force comprising of a few ships, a Kree Sentry, re-cloned Ronan, Yon-Rogg and some generic Kree cannon-fodder soldiers.
* Ronan judges. The Sentry sentries. Yon-Rogg slays a weakened Mar-Vell. Carol is very sad. Screams "Nooooo!"
* Carol's Air Force buddies join the party led by Rhodey in War Machine gear. Earth is saved.
* Re-cloned Ronan flees back to his planet in disgrace. Tells Supreme Intelligence thingy that they've underestimated the Earthlings (join the club) but it will be the last time. Camera sweeps back to see the majesty of the Kree forces in its entirety.
* Post-credit scene... more Thanos! ****!
Unfortunately, I think she might be involved in IW1 as a fully powered superhero, which would throw a wrench into the spokes of the above framework.