The stories I have read suggest that he did this in case the vehicle was booby trapped. Was this not legitimate action?
No. What if they were suicide bombers?
This violates the most basic elements of handling prisoners (also known as the 6 S's--Search, Secure, Silence, Segregate, Safeguard, and Speed to the rear for interrogation) that every Marine gets drilled into his head in boot camp.
"The stories I have read suggest that he did this in case the vehicle was booby trapped. Was this not legitimate action?"
It would appear that Pantano was standing only a few feet away from the vehicle as it was search. Had these guys been ready to detonate it, Pantano would have been fried with them.