Muslims can eat pizza.
There is nothing in the Quran about a food that hadn't been invented when it was written.
The Quran only says Muslims can't eat pork or carnivores, any other meat is acceptable as long as it is properly slaughtered. Bread, cheese and tomato are not meat. And there were clearly no concerns about the pizza not being halal, or Callen wouldn't have eaten it, Gloria wouldn't have asked to have some, and Jamal wouldn't have had to see if Callen was left handed to know he was an impostor.
Cops aren't allowed to kill people who pose no threat.
Shooting an unarmed civilian, in the back, while he's running away, would be murder.
The episode begins with a van carrying the terrorists being pulled over by a police officer for having their music too loud. Given that the terrorists are trying to keep a low profile it wouldn't make sense for them to be playing loud music as that would attract attention.