I would say "yes". Make sure that the disconnect ahead of the ATS can carry the locked rotor current for the fire pump. See NFPA 20 for calculation of the locked rotor current; don't use the usual rules of thumb.
As augie47 mentioned, the ATS is usually a combo with the fire pump controller. That way you can be sure that all the particulars are correct since we are dealing with a fire pump, and they are always a bit confusing. You could keep the upstream disconnect if you get a combo controller and ATS, but is also comes with a disconnect built in, so, why bother?