The first time I used leaf hops instead of pellets caused me to rethink my whole approach to hop additions. I wound up with a plugged up pump and 7 gallons of wort instead of 11 at the end of the brew day. I found bits of hop leaf matter for three brews after that, and I'm a cleanliness nut. I can look back and laugh now...
Whether using whole hops or pellets, I use hop bags. Don't fear the sack

I've come to prefer pellets for my system, but when they aren't available I go to leaf hops. I've also added a bazooka screen to my keggle. Knowing that whirlpooling isn't as effective in a keggle, adding the screen has given me further piece of mind. I have also begun using a Blichmann Hop Rocket (with either rice hulls or hops depending on style) in the recirculation loop of my JZ-style whirlpool chiller to help clean things up.
All that being said, things work very well for me. My wort is clear enough that when making a lager, I whirlpool chill with the Hop Rocket and a Therminator in the recirculation loop to help chill the wort quicker (and get some benefit from whirlpooling) and then switch from ground water to a recirc'd ice bath through the therminator to get my wort down to lager pitching temps. I do all this without clogging the therminator, so something is working

~widget