My reading is that the reef is submerged around 4m & 12 miles long but otherwise 60-80m depth. Wasn't suggesting they cant the keel & try and shoot over the top, just that if they felt confident in their information/location they would have been comfortable going relatively close.
I'd say the navigator was initially confident of their track but when they received the email they panicked as they could then not be sure where it was. Guess they only have the one brand of navigation equipment on board so not able to cross reference with what the email said & ended up going far enough around to be sure... Although Brunel would have been within AIS range so they would be able to see the track they had taken - but maybe their info had them thinking Brunel had gone too close. The dogleg was around 12 miles side-side.