Given that it's counter-productive to sanction quitters heavily (they'll ruin WZs worse by afking instead), it makes sense to reward those who arrive late to a warzone as compensation for truncated play and fewer rewards. Otherwise they're being penalised for someone else's selfish decision to quit out.
Something like a flat 10 comms bonus for backfilling, awarded at the end of the WZ, would be great. Nice little reward, but not so great it would make people quit and requeue in the hope of getting it.
I support this idea. I don't rage quit and I don't mind backfilling. On my Sorc, it's easy to get one medal for healing, but not every class has that ability. I joined a Civil War match last night after the other side had gotten a triple cap. It was hard to get that one medal in time! On other occasions, I've backfilled with not enough time to get that one medal.
Backfillers should get a small base reward for sticking it out.