When Google scans a page, it looks at all links, embeds, etc. It will see the script address for the embed. After they decide that the script is taking up too much CPU (user reports and whatnot), they will flag it as malware. Any page that embeds the script will also be flagged as malware. This can lead to things like pre-visit warning dialogs within the browser.

Hiding the script, along with any related content, from bots such as Google is the only way to prevent a page from being flagged.