In episode 15, it shows a man with a gun at his throat. I never new it was Mustang until just recently. Is that why Roy protected Marcoh when he ran off?

well i dunno about that but i do know why Mustang had a gun to his throat...
*SPOILER DONT LOOK IF U DONT WANNA SEE*
Mustang had just killed two completely inocent people two doctors... uh they were Dr. and Dr. Rockbell i'll leave it at that...XD