First, Alejandro doesnt actually kill Faustos family. Instead, after asking them to continue eating, he tells the cook to take them away from here and gives Fausto an option: You may choose to die tonight or live with the shame of having the mother of your children take your place. While Fausto chooses the shame of living, Alejandro still kills him and tells his wife, Maybe you take his money and go hide and raise your children far from here. Maybe your son grows up to be a doctor. And I dont have to come back and kill him some day. This certainly hints at the cyclical nature of the drug warfare, but the decided-upon ending has a far greater impact with its unexpectedly chilling, merciless nature.
As for the penultimate scene: Alejandro still shows up to Kates apartment, but there is no waiver for her to sign. Instead, after taking apart her gun, he humiliates her by lifting up her shirt and exposing her breasts, pointing out the bruises she endured when he attacked her. (In the original script, shes shot six times by Alejandro and he shatters her nose.) He then gives the monologue thats mostly beat-for-beat in the original conclusion. While its not a major difference, this ending might have gone a bit too far, given that Alejandro sticking a gun to her head is enough to prove Sicarios point.