It's maybe the 'wrong' way, but it works: when I need to do something similar, I first do a preg_replace_callback to find what I don't want to match and encode it with something like base64.
Then I can happily run an ordinary preg_replace on the result, knowing that it has no chance of matching the strings I want to ignore. Then unscramble using the same pattern in preg_replace_callback, this time sending the matches to be base64 decoded.
I often do this when automatically adding keyword or glossary links or tooltips to a text - I scramble the HTML tags themselves so that I don't try to create a link or a tooltip within the title of an anchor tag or somewhere equally ridiculous, for example.