Most soil fertiliser today comes from fossil fuel. This was the whole Haber Bosch breakthrough. If we give up artificial fertiliser and need to use animal manure, that would not justify the unsustainable scale of livestock we have today. There are also alternative sustainable nutrient sources like compost and seaweed. I don't know how much manure can be replaced with alternatives but I don't think your point lets us conclude that we absolutely need a meat industry like the one that exists currently.
Seaweed has salt. I you put salt in a soil you will ruin it for agriculture. In the first years there are a few salt tolerant vegetables that you can still culture. After a while the accumulated salt will be just too much even for asparagus.
Compost can help. I don't know how much that would scale in any case.
Is true that we can produce some fertilizers chemically, but we need to invest huge amounts of energy for this; After Wikipedia >1% of all the energy that we humans use in the planet is spent just to make ammonia, and many of this is used to make urea. If I'm not wrong we need also natural gas to feed the process, so this energy came basically from non renewables. Is part of the solution but not a miracle cure.
