Just to be clear here, you can modify VPK files for your server and it will carry over to clients, even if they have different versions, as long as you turn off sv_consistency. As Lux said, all vscripts are server-sided, so a client can have script.nut that has different content from your server's script.nut and the server would just use its own version.
Originally Posted by 404UNF
It'd take me about a minute to do it
Extract contents from VPK into a folder using GCFScape, delete .nut file, click and drag folder onto vpk.exe file in like, steamapps/common/Team Fortress 2/bin, done. VPK.exe generates a new VPK file of the map and whatever else, minus the .nut. Or, better yet, modify the .nut to make it harmless. I doubt the map requires the files existence to run. I'm not sure what a .nut file is either, nor am I sure how it would even get initialized (unless there's some entity in the map that calls it somehow?), but it sounds fairly easy to remove the damn thing outright.
My point is that some server owners are ignorant to these things, just like how writing simple plugins can be complicated for many users.