Broadband,
Whilst I entirely agree with your sentiments, we do work for a service industry and it would be wrong not to apologise for a delay, no matter what the reason.
I think they are being polite rather than shoe shining in this instance.
What they should do (and maybe they did) is apologise for the delay but also explain that the delay was for good reason and at no time would CX/KA jeopardise safety and security for OTP.
If any of the recipients don't like that, then yes, you are correct, they are just ignorant muppets!
However, the flight crew on the flight in question received what must have been in excess of a dozen compliments and thanks from the pax as they reboarded the aircraft. So, clearly, most of our pax appreciate the apology almost as much as they appreciate the concern for their saftey that overrides everything else.