You might be better off looking for a different free hosting provider. There are other free certificate providers, but they mostly use the same technology that Let's Encrypt does!
This anti-bot Javascript was presumably put in place by the hosting provider. If they won't help you disable it because you're not paying them, you might want to pay them, or else use a different provider that doesn't have this restriction.
You could look at this thread to find web hosts who support Let's Encrypt:
(Some of them may have free-of-charge hosting options that still include support for Let's Encrypt.)