hmm... i personally think the MSR feels more reliable than the Hiker. Although mine Katadyn pocket feels the most reliable (and heaviest too!). The MSR has the added advantage being field cleanible. So what failed on your MSR ?

I keep mine dirty water hoses in zip-locs. I even store some of mine clean water hoses in seperate zip-locs aswell. You can attach you waterfilter to many hydration packs directly, which also prevents cross contamination.

The filter which has the greatest cross contamination are the gravity filters. The kind you suspend with a waterproof bag. The dirty water that gets on the outside of the bag, will follow gravity and will eventully follow the clean waterhose to it's destination. Wiping it dry on the outside or scoop water with a cup in to the bag, does seems to solve that but is a serious hassle. Unless you have a few extra pair of hands.