Since epidemiology is well outside my area of expertise, I have to ask: would this be safe?
With artificial fertilizers we don't have to be concerned about the purity of the material, whereas if we were to use natural fertilizers (animal or otherwise) it introduces all of the impurities and other undesirable byproducts that come with waste. And if we're talking about human waste in particular, does that mean this would create a new cycle for pathogens? Or is there a way to process waste to remove pathogens?
Having recently become much more educated than I used to be on this subject, I now find it hilarious (and a bit frightening) how disconnected modern society has become from good old Mother Nature. If you'll stop and think a moment you'll realize that we live on the surface of a planet where quadrillions of living organisms have been living, dying, urinating and defecating for billions of years, and until a veritable blink-of-an-eye ago there were no "waste treatment facilities" anywhere to be found. The very fact that our civilization requires artificial "waste treatment facilities" in order to survive is a symptom of just how totally disconnected we are from the natural cycles of life. Every living thing that has ever existed here for billions of years has lived by recycling nutrients from the bodily decay or waste products of other living things.
So, asking "if there is a way" to process waste to remove pathogens is a question that should answer itself now that we are all in the correct mindset. The answer of course is that nature _is_ a gigantic and unbelievably effective and efficient waste reprocessing facility. Step out of the door of your artificial housing construct and walk to any nearby location where you might be able to grow a plant and look down. That stuff underneath your feet is called "dirt". It's composed of minerals extracted from the air by plants, leeched out of rocks by water, and more rock bits ground up by glaciers. But most importantly it's composed of lots of chemicals and compounds that either used to be part of the body of some animal or plant, or was a waste product of a living organism. If dirt, the infinitely reprocessed waste product of billions of previous excreting organisms, was going to hurt us we'd already all be long dead.
The bacteria and other organisms that live in dirt evolved to live on the kinds of things we refer to as "waste". They reprocess it into yummy fertilized soil that plants love to grow in, and in the process kill off all the things we call "pathogens" that evolved to live inside us and are excreted in our waste. The worms and soil bacteria and the eventual heat of the full composting process creates a perfectly safe fertilizer from any kind of animal "manure", including human. They even have a name for the manure that comes from us: Humanure.
Using this purifying ability of nature, we can even make cheap and highly effective water filters that work by letting the soil bacteria in a column of sand kill off the "pathogens" in contaminated water as it trickles through the filter. The soil bacteria just gobbles up and destroys everything that we would refer to as a pathogen. Chemical toxins of course are a different matter. Many of those are unnatural to the environment and have to be dealt with in other ways, unfortunately. But animal waste? No problem. Nature takes care of that quite easily.
Now, the issue of urine separation turns out to be interesting for multiple reasons. Using urine separating toilets not only makes it immensely easier to separately process and use the urine for fertilizer, it also allows one to have a composting toilet that doesn't smell bad and holds a surprising amount of waste before it needs to be emptied. Apparently that horrible latrine, RV/boat holding tank smell is caused not by the solid waste itself but by mixing the urine and solids. Separating the urine and throwing a layer of something organic like peat moss over the solids creates a toilet that at worst has a mild "earthy" smell, like a forest on a rainy day. There's a great composting toilet design for boats/cabins that works this way called the C-Head. I find its design and functionality much more appealing than the many non-urine-separating styles of composting toilets on the market. There are some super-gross YouTube vids of how such toilets, uh, "work".
There's a guy, Michael Reynolds, who has been building homes he calls Earthships for more than four decades now that require no public infrastructure connection. They process all the generated wastewater on-site using a built-in greenhouse full of plants and trees. Earthships don't even require a septic tank except to comply with some local building codes. And yes, that greenhouse includes food plants, and the food plants grown in wastewater are perfectly safe to eat. They've been tested by the same government facilities that test city water supplies and they come back with far lower levels of pathogens than you'll find in your local grocery store's produce. I'd highly recommend that anyone interested in this subject get some of Reynolds' books and videos. It's pretty fascinating stuff. They also do a lot of great work teaching people in super poor and devastated areas like Jamaica, Guatemala, Africa and Indonesia how to build their own Earthship type buildings for homes and schools. Like this. Good stuff. Also look for "Garbage Warrior" on YouTube. There's a full-length documentary.
So, yeah. Mother Nature is amazing, and we need to quit wasting mind-boggling amounts of energy inefficiently trying to artificially recreate what it already does just fine. Like processing "waste" (aka "nutrients") into "food". I mean, that's practically the very definition of what "nature" is!