Pork is prohibited not because they wallow in their own waste, but because in ancient times they wallowed in *human* waste. If you ever look at those archeological digs they do at ancient cities in the middle east, they weren't very clean. Peoples idea of taking out the trash then was to simply dump it out the window in to the street. This is partly
why Tels formed. Centuries worth of garbage and trash built up over the years and slowly raised the level of the city. Sites occupied for >2000 years had a lot of garbage pile up.
Because pigs rooted through human waste it was much more likely that meat from pigs was infected with some paracite that affected humans. This is that same reason why one *never* fertilizes a field with human waste. So what if the crops we grow or the meat we eat is infected with a cyst that afftects cows. Our immune system can handle it. But it was much more likely that pigs were infected with something that was harmful to humans.
Anyway, over the course of a few centuries people noticed that people got sick when eating pork, so they prohibited it for religious reasons. Even though conditions aren't the same today this has still carried over. Their loss. Modern pork is no longer unclean because we don't let the animals roam around in an unclean environment.