Wallabie - actually, it was an overrun and the point with that episode was that the crew landed heavy without flaps ... which caused the overrun. It was, however, an extremely good example of poor CRM.
The rules are there for a reason, otherwise everyone would be operating on gut instinct as to allowable weights - and that just isn't acceptable. I saw it many times in my African days - there were some highly skilled pilots who really pushed the envelope ... and some pushed it too far. When you're doing that with other people's lives it is not acceptable. This is clearly what happened on this occasion.
As you say, Air France were wrong not to have fitted the protective panel to the landing gear - not just because they probably didn't want to save money, but because it was an Airworthiness Directive.
And finally, he wasn't "200kgs" overweight. He was 2,130kgs over the MTOW and 6,000kgs over the RTOW. That's clearly unacceptable, in anyone's eyes.