I decided to time the Starbuck-shoots-Boomer scene.
Starbuck becomes aware of a figure standing above the pit and slowly looks up to see Boomer. Helo turns his head to see what Starbuck is looking at, then he turns back unconcerned and says, "Hey, I..." It takes Starbuck only about a second to glance down to look for Helo's gun, but it had been 5 seconds since Starbuck had looked directly at Boomer. It is another 4 seconds before Starbuck fires, because she is having to struggle against Helo.
So Starbuck's timing went something like this...
tick - Recognizes Boomer and realizes she is not Galactica Boomer.
tick - Concludes Boomer is a Cylon.
tick - Decides to kill her.
tick - Realizes Helo has the only gun. Helo says, "Hey, I..."
tick - Concludes Helo doesn't know, plans to snatch Helo's gun from him.
tick - Looks for the gun.
tick - Grabs the gun.
tick - Struggles with Helo.
tick - Yells, "She's a Cylon!" and fires.
Then there is the question of why Starbuck screams. Helo says, "No no, you can't, you can't. She's pregnant." He has Starbuck's weapon hand pinned against the wall, and she screams while trying to summon the strength to struggle against him, but she cannot break free. The weapon falls to the floor, and she sinks to the floor and cries.