I mean, you don't have to start with 0, nor does the fact that we had more bison emitting (for the sake of argument, although given all the deforestation, petrochemical use, and other agricultural processes involved in sustaining modern cows I'm not sure it's a given, especially when taking a global view) more methane in the past excuse the damage of the methane emitted by current cows.
We could have had X units of CO2, and Y units of CH4 produced by bison under the past era.
We've eradicated the bison, replaced them with 1/2 their number in cows. We now have X units of CO2, Y/2 units of CH4 produced by cows.
This is still producing more warming than if we eliminated the cows, and went to X units of CO2, 0Y units of CH4 produced by cows.
The existence of the cows still results in more CH4, and more warming, than would be the case if we phased them out, no?
In any case, if we replaced the cows by food sources that produced less than X + Y/2 units of atmospheric CO2 and CH4 respectively, we're better off.