Yes- I'm flying SEA-LAX on AS (and getting my full elite benefits), LAX-JFK on AA (and using a voucher for the ticket + miles + copay to get a business class upgrade). I'm not particularly worried because there's a ton of time between the flights (I did it this way to get a longer layover in LA), and if my flight went mechanical or something, AS flies a LOT of planes to LAX- there's plenty of time built into the schedule.

I also mix and match carriers on roundtrips- AS SEA to LAS, DL or WN back, VX SEA to LAX, AS back.