Thank you for your post into the forum.
At this time there is not an option to ignore SQL Print Statements. Therefore I have added the details of this forum post to an existing Feature Request whose reference is SC-3522 and set the request for review.
I recommend that you also post your request on the SQL Compare User Voice Forum via this LINK.
The more votes the request receives from other SQL Compare users, better the chances of seeing this feature appearing in a future version of the product.