Pretty certain the coffee roasting process takes care of all of the germs and mold. Either way, if this guy really cared about the conditions his food was in before it reached his table, he'd be limiting his diet significantly. Agriculture is dirty work. Some of it is dirtier than others, especially if we're talking about animals.
Case in point, pork. Ever been on a pig farm? Not a farm with pigs, but an actual pig farm? I know a guy who owns one and he tells me those fuckers are dirty, and I don't mean wallowing in mud dirty. I mean if you go into a building with 1000+ pigs, you will be overwhelmed by the smell. If you're there for any length of time, it permeates your clothes and your skin and you won't feel clean until you scrub like crazy. Know what smells delicious though? Sausage. I rest my case.
Had a boss who used to work in Idaho, designing AV systems. He got called onto a chicken farm once because they needed an audible alarm that could be heard 100 yards away. Apparently if the vent fans in a battery barn go out, and you don't have the secondaries switched on within a minute, the chickens all asphyxiate from the ammonia.
Which means, effectively, that battery barns output a 100% lethal stream of ammonia 24-7.
There's something subtly magical about the wikipedia article on chicken manure.
Edit: Also, Imigongo.