I think the point is that Silva was playing with Bond. He figured Bond would be better than his thugs, so he wanted to see what Bond would do, and have Bond burn his booby traps and whatnot. Then Silva makes his dramatic entrance with a helicopter, after Bond had is “is that it?” moment. It’s cat and mouse time.
He didn’t know about the tunnel, so he was hoping to flush them out, and thus have his final face to face with M. Of course, burning her in the mansion would work as a fallback option. But the tunnel got M out, and Bond outsmarted the helicopter with a propane tank (:dubious:), and then Silva saw the flashlight.
Apparently the helicopter was an AW101. It is not a missile platform or gunship, it is a transport vehicle. It is a kind of assault helicopter, for putting soldiers on the field or evacuating groups. It is not armed with forward-facing pilot activated weapons (at least not Silva’s), but did have a .50 caliber mounted in the crew compartment. Thus when Bond starts shooting, the helicopter pivots sideways before the .50 cal can shoot back.
And again, Silva didn’t want M shot by the .50 cal, he was yelling at his men that they were not to touch her. He wanted to be the one to kill her. The firebombs were a flushout technique.