WordPress Multisite disallows the unfiltered_html capability for non-super-admin (ie, any users who are not capable of performing network administration). Anyone without the unfiltered_html capability will not be able to save post content with disallowed HTML tags, including <script> tags.
A quick search shows that there have been attempts at modifying this behaviour, but they may have been invalidated by subsequent updates to WordPress core.
See this answer for a possible solution (though it may not work anymore.)
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