I think they just stuffed up the wording. I think the whole "can't use it to create a commercial database" means you can't use the document itself (i.e. "this material") as part of your own commercial database offering but you can absolutely adapt the protocol and share the document that Mongo created under the same terms (i.e. share-alike).

Because it's already in source form and isn't "compiled in" into a derived form I don't think it has the same potency from an infectious license perspective as GPL does. If you bundle this document as part of your commercial database I think they can't do diddly squat as long as you make clear that the document itself is still under the CC sharealike license.