A fix I would consider is to have the inputs more thoroughly checked for correctness before passing them on to the ATC system.
Thoroughly checking of the inputs as far as possible should be a given, but in this case, the inputs were correct: while the use of duplicate identifiers is considerably less than ideal, the constraints on where that was permitted meant that there was one deterministically unambiguous parsing of the flight plan, as demonstrated in the article. The proximate cause of the problem was not in the inputs, but how they were processed by the ATC system.
For the same reason, multiple implementations of the software would only have helped if a majority of the teams understood this issue and got it right. I recall a fairly influential paper in the '90s (IIRC) in which multiple independent implementations of a requirements specification were compared, and the finding was that the errors were quite strongly correlated - i.e. there was a tendency for the teams to make the same mistakes as each other.
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This might not be the reason why the developer chose to have the program essentially pull the fire alarm and go home in this case, but that's the impression I got.
I mentioned elsewhere that any ATC system has to be resilient enough to handle things like in-flight equipment failure, medical emergencies, and the diversion of multiple aircraft on account of bad weather or an incident which shuts down a major airport.
As for why the system "pulled the plug", the author of the article suspects that this particular error was regarded as something that would not occur unless something catastrophic had caused it, whereas, in reality, it affected only one flight and could probably have been easily worked around if the system had informed ATC which flight plan was causing the problem.
It would be interesting to actually see the code.
All using communication links and protocols that have evolved organically since the 1950s, need global consensus (with hundreds of different countries' implementations), and which need to never fail.
The affected flight could have been vectored by ATC if needed to divert from filed FPL.
Way less work and a better doutcome than the “system throws hands in the air and becomes unresponsive”.