While I don't love the poacher storyline, it serves a purpose, so I think it should be left alone.
Even though it may be a bit upsetting now, and may jar people from their Disney comfort zone a tiny bit, educating children about the realities of animals and their lives may help them to make better choices later. I know it sounds silly, but I'm sure all the animal rescue workers and explorers who do such great work to preserve and protect animals today were inspired by *something* at some point to make them choose that career. Why not a "cheesy" theme park ride?
I agree with a previous poster that it fits in well with AK's theme of conservation and preservation. Granted, they could probably figure out a slightly better way to make it more compelling and less disturbing to some, but Disney on the whole is so clean cut and sanitized that I find it a bit refreshing that they do deal with the reality and educate people about it. I'm sure a lot of us never gave any thought or were even aware about ivory poaching before we saw the attraction.
However, I don't have kids, and I'll freely admit that I might feel differently about it if I did- I'm sure parents feel very differently about things that may overstimulate or frighten their little ones, so I really can't judge that.