Hi Matěj!
Since interwiki links in Wiktionary are handled by the Cognate extension and not by adding pages to Wikidata items, it should not be possible to add those pages to items. If I understand correctly the way to achieve this is to create an edit filter preventing those edits, and it seems that you are by far the best man for that job.
What we need is a filter that prevents adding sitelinks to pages in the main namespace in Wiktionary. All other namespaces (except User:, of course) should be fine. Is this something you can make?
Also ping to Aude, who might have some input here.