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Sure. Why not add an equal amount of cinnamon?
Your donuts won't have the same taste as those made with nutmeg and might be bland if you just eliminate it. You can replace the nutmeg with another spice you do like and have at hand. Cinnamon, ginger and allspice come to mind but since they are your donuts, you can flavor them with any spice you like. Consider lemon zest, which technically isn't a spice but when finely grated acts like one. You would have lemon flavored donuts which, at least to me, doesn't sound like a bad idea.
Have you tried fresh grated nutmeg instead of the spice aisle stuff? The flavor difference is dramatic.