Antimatter negates Fahrenheit's base attack. Then Fahrenheit's ability activates and adds that damage to the weapon's base attack. So if Fiery is adding 5 damage then Fahrenheit will deal 0 damage total.
Antimatter does not also invert the ability's damage nor does it stop the ability's damage from being calculated into the total damage.
However, as I recall Fahrenheit did used to heal 5 damage before inflicting the rest of the damage. Because Fahrenheit was still dealing damage while Frozen, however, the effect damage was added to the actual weapon damage to remove that bug.
