It has a 4.5 inch cannon, a pair of 20mm cannons, two quadruple Harpoon (anti-ship missile) launchers, two torpedo tubes, a Goalkeeper anti-air/missile system and a two Seawolf anti-missile systems. There will also be numerous small arms on deck - usually 7.62mm GPMGs, Browning .50s and miniguns.
Although I don't know the exact details of this incident, it seems likely that the boat was some distance away from the frigate, and certainly out of sight. Assuming the marines managed to use their radios before being picked up, the frigate would have taken a looong time to weigh anchor and get the ship moving. Helicopters were dispatched and they spotted the marines being escorted towards Iran, but even assuming the helicopters had appropriate armaments, they couldn't start shooting at vessels with British servicemen on board. Also, there were six Iranian ships. Again, I don't know what type of ships these were but I know they have some decent stuff from the UK and USA, so if I was the captain and I got a call saying 6 ships had just stolen a bunch of marines and headed off into Iranian waters, I wouldn't want to go chasing them down with my one solitary ship. Better to wait for Them to turn up and bust them out, or leave it to the diplomats.