In the beginning fight scene, none of the crew Cap engages with would be considered kills as all looked to be incapacitations only.
7:06 Rumlow shoots a guy
8:17 Widow shoots 2 guys and then a third as she chokes the 4th while dropping down
8:23 She shoots 2 more
10:29 Five guys shot in breach of hostage room
29:19 Fury shoots 9 undercover hydra
29:42 He gets another
31:13 Fury squashes guy with his car
31:18 Fury knocks another guy through a store window with his car
32:14 Enemy car is sideswiped likely killing 2 guys
1:06:19 Arnim Zola AI destroyed
1:08:59 Housekeeper shot by Pierce
1:16:42 Sitwell thrown out a car
1:20:03 Falcon knocks guy off bridge
1:20:07 Cap deflects gunfire to kill a guy
1:20:12 Falcon shoots guy from bridge
1:20:32 Police car blown up killing at least a driver
1:36:43 Hydra shoots 2 guards
1:38:24 As a fight between Hydra and Shield that sees 1 and 2 killed respectively
1:38:58 Hydra shoots 5 shield guys taking a carrier
1:40:08 Cap takes out 3 Hydra with a grenade
1:42:01 Falcon guns down a guy
1:44:37 Winter gets 5 Shield guys with a grenade and then another 2
1:44:43 Winter shoots a guy in the throat and then throws a grenade getting a guy in a plane
1:44:49 Winter kicks a guy into a turbine and then kills a pilot of another plane
1:47:25 Hill shoots 2 Hydra
1:48:56 Rumlow kills 4 Shield guys
1:50:54 Pierce kills 3 bureaucrats
1:55:29 Fury kills Pierce
1:56:17 Two of the 3 Helicarriers go down
2:00:15 The last Helicarrier goes down. We can safely assume that each of them has roughly the same crew and we clearly see a commander and second in one several times, also as one takes off we can see 11 crew clearly on the deck. They likely have more than this, but there is nothing to confirm numbers so each has at least 13, thus the subtotal of the 3 helicarriers is 39.
Here is the Body Counts kill count. It is a little high because they count several ‘kills’ from Cap’s attacks that clearly didn’t kill the target and their estimates on the number of individuals on the Helicarriers are higher than mine though I can’t see where they got their estimates from.
The Carnage Count is a little lower than ours. This stems from a couple of different reasons. Like the Body Counts kill count, they over estimate the damage Cap does, but Carnage did not attempt to estimate the number on each of the carriers (understandably).