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If hyperlinks are "greyed out" in the toc portion of downloaded samples from the iBooks store, I'm sure that's just part of what makes a sample "a sample." I can't imagine you would have to "do" anything (as the ebook creator) to achieve that.
If you just want a non-functional html toc, you'll have to remove the links from the code: manually or with a some sort of regex expression.
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