I don't think there is an issue with the course going thru "Rk" when your yacht draws 6ft. We have some similar rocks near my marina which are about 5m (16ft) down when the surrounding water is 7-10m deep. These rocks are actually marked as a "reef".
However in the circumstances you described I would of done exactly the same. At night in an unfamiliar area I would of altered course as well. If it was daylight and I was familiar with the area I may of cut the corner.