I have dived this reef (the day after I gained my open water) and it was a wonderful experience, I was lucky to have fantastic conditions and my buddy was the instructor who had just done my training. I am sorry your experience wasn't as good.

On the subject of certification,I don't know what happens at other dive schools but at the Red Sea college where I did my PADI there were a few people who were failed either because they couldn't do some of the exercises ie. mask removal underwater or they didn't do it confidently enough. My intructor made me do the techniques over and over even if I "passed" the first time.