Then you can just declare your subs in packages, as others have already said. To overwrite your own subs, users would need to name them with their fully qualified name, e.g. package Plugin; sub Core::overwritten_routine { return "foo" }. That is rather hard to write by accident.
After that, the only thing I can see to prevent (probably malicious, at this point) users from overwriting your subs is whipping up some PPI and checking any source files you require before actually requiring them. With your setup and in your environment, the hassle is probably not worth it.
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