Ok, so let's say the lowest externality food will be a baseline. For example peas. Grains are higher, so we would also tax grains? And we would grow this until the highest - beef. Or is there going to be "accepted externality"? If so, why those who suggest taxing meat more suggest the cutoff right between plants and meat?
For the reason you give, a Pigovian tax on the externalities themselves is a better approach than specific regulations or pre-defined taxes on each class of consumer product.
Another benefit of this approach is that it provides price signals to the product's producers as well as consumers -- after all, if a company comes up with a way to produce beef with fewer externalities, they should be able to capture some of the value!
There is certainly disagreement with regard to how to handle some of the more difficult-to-assess externalities, but even taxing a handful of externalities still helps push product prices slightly closer to their true cost.
Another problem is that taxing negative externalities is often used for another things than eliminating given externality.
I will buy beef (or corn). It will emit CO2. Capturing given CO2 would cost $5. So the tax will be $5. But politician will not use these $5 for capturing the CO2 emissions.
He will buy votes instead. $1 for a symfonic orchestra. $1 for police department. $1 to subsidies to a company of a friend lobbyist. $1 for a new playground... Most often, negative externality taxes are just proxy for taxing people more without using money to fix the externality. So even if you believe the externality exists, but you are not supporting given politicians' program, it is a rational choice not to pay the tax.
The primary goal of taxing a negative externality is to discourage it. Using the funds for mitigation would be a secondary benefit.
If you object to using tax policy to shape public behavior because politicians cannot be trusted to efficiently allocate the resultant revenues then perhaps you'd be in favor of returning the revenue as a dividend[1], which is an option that has become more popular lately.
