There isn't anyway to disable adding that link, which is a fallback style link for users that have JavaScript disabled for some reason.
It is valid HTML to include such a fallback (a link tag is permitted content, see hidden link), and has no implications for SEO.
(Some people abuse the noscript tag and stuff it with invalid content to—wrongly—try and boost SEO, which doesn't work; perhaps that is what your SEO company is warning about, but it is not what is happening here.)
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