Alan, it is a matter of philosophy. You COULD simply wire the bilge
pump directly to the battery (one or two, you'd have to choose) but then, if you smelled gas or propane aboard one day, you'd have no way to make sure the
pump didn't start and spark it off. Never happen? Maybe, but that's the logic of running it through the main switch, to ensure that "ALL OFF" means "ALL OFF" without exceptions.
A compromise would be to run it off the main switch--but install a separate switch (auto-off-manual) and fuse or breaker for it alone. That way "ALL OFF" is still "ALL OFF" but you the pump can be the only thing you choose to leave on.