I think this would be simple to do. The key is allowing the bag to hang while still allowing the water to gravity feed through the filter, and catching the clean water in a container. This is different from other gravity feed filters in that most have the filter element in the bag.

Another solution would be the Platypus CleanStream which uses the same filter element as the AutoFlow, but uses Playtpus bags to carry the water (dirty water bag and clean water bag). You could save weight by not carrying the clean water bag and catching the clean water in another bag/bottle. This would probably save about 5 ounces or so.

One added benefit to this filter is the filter element can be used as an inline filter in a hydration system. Because the flow rate is so good, there is almost no reduction in flow rate as the users sucks water from his reservoir. This is great to have for mountain biking in an emergency...