Since Windows 2000, there's a Registry binary key that allows you to remap keys just above the driver level:
HKLMSystemCurrentControlSetControlKeyboard LayoutScancode Map
Fortunately, there's also a GUI app which allows you to configure it easily, called SharpKeys (no affiliation, just a happy user). The remap is quite flexible, so far I've managed to remap every standard key (inc. Ctrl, Delete, F4, etc.), even the "multimedia" keys that are on some keyboards.
The app just writes the settings into Registry, so it need not be running all the time - and once you've found a layout that you like, you can just export/import the Registry key through Regedit, no special tools required.
I'd suggest to remap all the "dangerous" keys to something innocent - e.g. map Ctrl, Delete, and F4 to Shift.
CAVEAT: this is a system-wide setting, so if you'd ever need to press Ctrl+Alt+Delete in that system, you'd be out of luck (you'd have to edit the registry key again). Also, the mapping is read only once, after system boots, so you need to reboot to apply the changes.
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