From all that I've read, when you boil fruit or juice, the pectin will congeal. Instead of boiling, you can just steam it for less than a minute and that will kill all the nasties without doing too much damage. The nylon bag makes sense, but when I did the Raspberry Ale for my wife, I noticed that the chunks of raspberry were quite actively moving around in the secondary. When I racked to tertiary, I ran it through a nylon bag that was laying in a large funnel. The funnel had a hose attached so that the beer wouldn't aerate going into the carboy and I "sealed" the whole system with sanitized saran wrap.