If Duggan was the type of writer with long term planning, one possible route to the Mutants beating a super-powered Nimrod, is if Dr. Gregor develops a change of heart, begins working with the mutants, and manages to deactivate or distract Nimrod by appealing to the last remants of her husband. That would fit thematically (mutants and humans working together) and emotionally (she helped found Orchis and created Nimrod out of grief, but is has now moved to acceptance).
But of course, that wouldn't happen because Gregor is an underdeveloped character, and most writers/readers do want a climactic battle where the heroes correctly are the main characters and unleash their best powers. Even I have to admit, in this issue, to feeling satisfaction at seeing Colossus/Wolverine/Cyclops have little victories despite how dumb a lot of the setups are.