That's an interesting challenge because what you call File Explorer is also the Windows Shell. Disabling it would prevent the Shell from loading I would wager. Having said that there are a couple of options to limit the processes that can run on a machine.
The most obvious solution is to use Kiosk mode. This would allow only the one app (or on Windows 10 you can do several) you specify to run. This is most useful in kiosk apps but would be limiting if these machines were being given to employees to do work.
The second option is to use GPO to limit the applications that can run. This is the most common approach and allows you to specify the program(s) that users can run. But I've never tried to prevent Explorer from running because, again, it is also the Shell.
I'm not sure why you are concerned about limiting users' access to the file system but I would personally just use NTFS permissions to prevent access for security reasons and then configure the allowed list of apps (using GPO) and also the startup app (another GPO) so users don't normally work with Explorer. However if they do access it (say via the Open/Save dialogs) then NTFS would limit what they could do.