That's hardly a critique of the trolley problem. Special relativity itself stipulates that it doesn't apply to faster-than-light movement, but a moral theory can't say "certain unlikely or confusing situations don't count". The whole point of a moral theory is to answer those cases where intuition is insufficient, the extremes you talk about. Imagine where we'd be if people just accepted Newtonian physics, saying "It works in all practical cases, so ignore the extremes at very small sizes and very high speeds, they are faulty models". Of course we don't allow that in the sciences, so why should we in ethics?