On a thru hike I would combine the chemicals with a filter like the Aquamira Frontier Pro. The filter is light but does not do anything for small organisms, due to the pore size; however, it will clean the water of cysts, which tend to be the largest critters, and then you only need to wait for the chemicals to kill the smaller things present, giving you a much shorter wait time.

The Frontier Pro is about $25 and would fit in a bounce/resupply box - you could probably also pick one up at an outfitter in town along the way, could get a list of dealers from the Aquamira website.

The only chemical treatment I'm aware of with a warning about long term use is iodine - since it's not really effective for giardia and less so for crypto, probably not a good option anyway.
"In the beginner's mind there are many possibilities. In the expert's mind there are few." Shunryu Suzuki