Given the information provided, here is my take on what really happened.
Navy Divers attached the towrope to the lifeboat effectively capturing the watercraft.
After several days in the boat without medical attention, the wounded bad guy, mad with pain and probable infection was allowed by his compatriots to surrender.
Navy interrogators convinced the captured bad guy to get his bad guy buddies to exit the lifeboat with the good captain and sit on top of it.
When this occurred, somebody on the Navy ship gave a signal to the good captain to exit stage left the lifeboat which he did, by jumping overboard yet again.
When the bad guys pointed their weapons at the good captain, now bobbing like a cork in a bathtub, crewmen on the ship opened up with everything they had.
The bad guys, in all likelyhood, did fire at both the good captain and the ship when they suddenly realized the game was over.
Three shots, three kills, through the hardened glass viewport of a lifeboat, from and at bobbing watercraft, in the dead of night, is simply beyond the possibility of reality, SEAL Snipers or not.