Though Windows Server is very powerful(I know from working with it), it does cost a lot of extra money to implement. The licensing cost alone is outrageous if you want to set up some office workstations and some server boxes.
I think the main reason why governments are moving away from Windows is because it takes a lot more money to implement and upgrade. Or they could use Linux and only pay for hardware.
Linux can be more secure in certain areas, since the code is more isolated, it makes it harder for a virus to spread through the system. Whereas Windows once infected with a virus it can spread through the system using the kernel, it's a lot less likely with Linux. I've used Linux a lot and I've never gotten a virus on it, with Windows I've gotten uncountable viruses.
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