I think we can go with "GNU/Linux," but I do think we should have footnote indicating that it is sometimes simply abbreviated to "Linux" and make a similar note in the glossary.
I think that's a good way of dealing with this. Your OER handbook -- or should I say "our" OER handbook will carry the sanction of the freedom culture -- especially when the text provides an objective and NPOV.
Having the free culture network on your side will scale this project beyond your imagination!
I should note to both you and Kim that I've made the change to "GNU/Linux" where I've found just "Linux" and changed the glossary to match.
If anyone find mention of just Linux (beyond the footnote and glossary mention). Please change.