However I was under the impression that Mr Skipp was acting on information from the CAA, (not just his team) stating the runway was safe?
You're referring to a newspaper report from, I think, a non-specialist reporter, quoting someone whose credibility is being fairly conistently questioned by posters on PPRuNe.
In my experience, the CAA does not confirm that things are safe nor does it endorse work - at best it accepts that the proposals meet the rules. How this is perceived by the other party no doubt varies. What appears to be a weakness in this instance is that the CAA did not challenge the scope of the risk assessment. Nonetheless, the facts appear to remain that even when faced with serious incidents no significant action was taken to assure aircraft safety until the business' finances were affected.
In theory, the airport had to have a safety management system. In theory that SMS had to have been assessed in some way by the CAA and accepted. The CAA should then have gained assurance that the SMS was being applied and was achieving suitable results. Perhaps it is surprising that these points did not receive greater consideration in the investigation. The whole world seems to be going down the SMS route, at least in aviation, if it doesn't work then maybe a big rethink is needed. And yet the UK AAIB barely mentions it.