It's more of a practical concern.
Migrating the government to Linux and using a free mail infrastructure would be cheaper (saving money in the long term, instead of costing), easier, and way more effective than using a non-standard internal email protocol and keep using Windows everywhere. Why bother when Microsoft still has access to all your data?
About using that proprietary protocol AND migrating to a free software environment, that could be better than just migrating, or worse, depends of the actual quality* of the protocol. But while the government frames it as a XOR option, migrating to an open stack is the only sane option.
* The fact that the protocol isn't public isn't good, the fact that it's Serpro creating it makes this worse - they've already done quite a few bad decisions about security.