I can see that from a server maintenance point of view. After having read so many great things about NixOS, I may have exaggerated my expectation and I may be the problem for being a user with too limited needs to get the full benefits of NixOS.
For me this single config file doesn’t save that much additional files and most of them would be files you configure only once during installation. Nonetheless I can see how “easier” it would be to save one file instead of 3 to reproduce your system and I can only imagine how much better it is from a server point of view.
As others said, the fix will be easy. Reinstalling everything should never be something you have to do. In the very worst case scenario, chrooting should solve any situation. Contrary to other OS, even removing system files will not force you to do a fresh install from scratch.