It's not that they are consciously fertilizing with human waste, but that the water they are using to irrigate has human fecal matter in it.
From the information we know so far, the Hepatitis A infections seem to come from specific targets, i.e restaurants, where the green onions are delivered to.
It is easy to blame Mexican farming but looking at the facts, Mexican farms ship thousands of tons of green onions, if they were all infected, many more people would have gotten sick, and the infection couldn't be traced to a single source or restaurant.
JMO, it seems to be a targeted attack, either by a deranged individual or small scale terrorism.