I think rebrand is exactly what's going to happen. It's a shame but I just get the feeling that's what they'll do, as it will take a very long time for this incident to be forgotten, and because of the way the internet works info will still be floating around 1 or 2 years from now, easily.
Any time someone searches "Alton Towers" or "The Smiler" on Google, they're gonna get tons of results from news articles. Any time someone looks up on YouTube they're gonna get more of the same and probably footage of the incident itself. Its not uncommon for videos to pop up at the top of the YT results that were posted 4 or 5 years ago. The incident on RMT happened before YT really took off. We're in a whole different era of technology and social media compared to 2006.
Obviously merch will be destroyed.
Never really like the name "The Smiler" anyway but it was a pretty strong brand especially with the evil smiling face.