Manure is the least of problems on factory farms. Eventually the manure pile is shipped off to make fertilizer and/or energy. If it’s not, then they are leaving money on the table.
Manure is piled up like that for a reason: it traps heat and allows the pile to compost. Manure is not a good fertilizer until is fully composted which does not happen if it’s not piled up.
Even small family farms that use open field grazing and treat their cattle exceptionally well use farm equipment to pile up manure so it can compost for a year before spreading it on their fields.