A quick reply as we've probably both got other things to do...
Your argument for making the animal concern magically disappear is nihilistic: it's OK to do the worst stuff because defining 'worse' is a matter of prejudice? Well you can define yourself out of responsibility for any problem that way. It's similar to the process of dehumanisation by armies and governments of enemies that they want to kill. Animals rate higher than smaller animals and plants, except when someone queries the animal comparison then the plants are invoked as equal to the smaller animals in the name of avoiding prejudice. Nah, can't accept such an argument even if 'plants' are then disguised as 'land'. Changing values..
"Everything ties together. Vegetarianism works as a model where motive is the immediate suffering of an individual, but falls when discussing greater ecological systems, net gains and losses etc." Even if this were true it would still be the case that in practice the more people stopped eating meat the better. But there seems to be no fundamental reason why it should fail. You argue in terms of animal fertilizer but don't say why you need to kill all the animals to get the fertilizer. Other methods are doable (as you say) on manageable scales. You do touch on the problem arising from the scale of the requirements - " but not successful enough to feed enough ". But the acceleration of human reproduction would ultimately destroy any system (more or less what we have been seeing in recent years, in slow motion). If you are arguing ultimate, steady-state systems you have to recognize that fact and not bomb out viable systems due to this universal constraint.