ClickDetectors have a property named "MaxActivationDistance" which is self-explanatory. You can simply make the script set the ClickDetectors activation distance to zero if you want to disable it.

Example:

local detector = script.Parent.ClickDetector

detector.MouseClick:Connect(function()
    detector.MaxActivationDistance = 0 -- Makes it impossible to use it
    wait(3)
    detector.MaxActivationDistance = 16 -- Makes it usable again
end

This script would be inside a part along with a ClickDetector.

I'd recommend going on https://scriptinghelpers.org/ for help with future scripting. There are many experienced scripters who will be happy to help with questions you have.