I'd stick with a proven filter with reliability and field maintenance foremost in mind, something bombproof and easy to take care of will remove a huge risk from the trip. There are too many variables with the steripen for me to trust it on a critical large trip, particularly if one of it's internal components breaks down in the field. Hard enough to get one of those repaired or replaced stateside.
I'd also pack a large supply of backup water purification tablets, chlorine dioxide preferably to avoid mixing (does chlorine dioxide kill the South American bugs? I assume so, but it's worth researching). Weight is negligible, benefits are high.