wals.info confirms that pretty much all "small" gender-like systems that don't have a masculine/feminine distinction use an animate/inanimate distinction. A simple way of differentiating your conlang from the usual fare presents itself here: a two-gender system that is neither fem/masc or anim/inan. Let's establish two end-points- all humans belong to gender 1, all mass nouns to gender 2. However, this is not a count/mass-distinction either.
Nouns that are neither human nor mass are arbitrarily distributed between the two. Nouns that are both - crowds, tribes, etc - can behave as members of either class.