It's true that methane has a much greater impact, but only in the short term. Long term, CO2 is much more dangerous. The methane that cow produces is recycled as it circulates through the atmosphere -> plants -> cows -> atmosphere cycle. Fossil fuel burning on the other hand is not. It's released from the ground and there's no way for it to get back there.
Nothing is ever black and white and to think that eliminating the animals as the food source would solve the problem is naive.
It's short term (12 years seems like before being reabsorbed) but this also means that we have this big static-ish chunk being renewed and absorbed in a cycle. If we reduce emissions then that static variable goes down and gives us more time on the other 100 things we need to figure out.
CO2 from fossil fuels can also be reabsorbed by plants. If you grow a forest, chop it down, bury the logs, then it's underground again. Although, not sure why you need it to be underground as long as it's not in the air.