I’m totaly agree with you.
What you can try also:
Customise the website Doctype and add a check field called for e.g. “use head script”. I believe this field value should get loaded by the get_context function of the webgenerator. then you could insert your script between the jinja tags “{% if use_head_script == “1” %}” and “{% endif %}” in the base template (“base.html”) of frappe.
If this field effectly get loaded by the get_context function, your code will be insert by the generator only if you checked the check field in the website record.