"This was an organisational, not a technology failure. "
You are probably correct here, but:
"Fixating on "Microsoft versus Linux" isn't just juvenile, "it's also counter-productive. "
This was probably the reason why there are any issues with this rollout to begin with. It is most likely the non-technical elected Munich council/mayor who use Windows at home and don't want to have to 'learn something new' who are the problem. So yes, the problem is organisational AND it's most likely a fixation of some people who don't want to use 'this other stuff'. The hallmark of poor leadership which doesn't take advice from their subject matter experts.
"If there's one easy lesson from this, it should be that Linux's proponents really need to stop pitching Linux as a "cost-saving" alternative to proprietary software"
Unfortunately that is the main reason most organisations will be tempted to switch as most people who are supposed to be plotting out the long term strategy of an organisation, fail to take into account that handing over the critical infrastructure of your organisation to a convicted monopolist is probably not a good thing to do in the long term.