We don't currently have an option to exclude Bookmarks though it is on our development to-do list. For now you would need to work the other way round, tagging recipes that are definitely gluten-free with your own gluten-free tag.
Our instructions to indexers re exclusion diets is only to add the tag if the author specifies it as so. This is for a couple of reasons. Firstly to avoid the potential minefield of what is and isn't truly excluded. And secondly to avoid recipes getting multiple tags that really are not relevant e.g. a stew wich is gluten-free, dairy-free, egg-free, low-carb, low-salt, low-sugar, low-fat, etc. when it could reasonably be expected the recipe would be all those things.
The best way for you is to create your own search parameters that work for you by using Bookmarks. If you go through your indexed cookbooks adding tags such as Gluten-free, Could be GF (where you can sub GF ingredients) or whatever you need, then use the Bookmark filters when searching.