Specific times and circumstances that deaths occur
12:26 Skrull is shot
12:54 Another Skrull is shot and then 4 more with a single energy bullet
13:10 This is where the first major engagement starts between Kree and Skrulls which ends at 14:10. In it 13 Skrulls are killed.
21:12 Two Skrulls are blasted by Danvers
21:30 Five Skrulls are sucked into space
33:23 Skrull posing as Coulson is hit by car
1:09:03 Mar-vell is shot in flashback
1:19:21 Science Skrull is shot by Yon-Rogg
1:34:06 The Flarkin eats 4 Kree
1:36:50 Talos shoots 3 Kree
1:38:22 Two Kree are sucked into space
1:40:15 The Kree pilot chasing Rambeau and Fury shot down
During this sequence, Captain Marvel destroys several individual ships, but it is unclear if they have pilots and look more like drones, so no kills will be counted here.
1:43:00 An entire Kree Warship is destroyed. It is impossible to estimate the crew of this ship. A similar ship is destroyed in Guardians of the Galaxy, but neither really gives a crew compliment. Plus it is impossible to know to what extent the ship is staffed compared to what it should be. The most we can assume is a captain and a second in command.
Total: 41