Thanks to Safari's reading list, I'll likely stop using the Instapaper bookmarklet on my iPad. But the most common use case I have for Intapaper is when I see an article on my laptop in Chrome and want to read it later on my Kindle 3. So I expect I'll be using Instapaper for a while longer.
This is a generalizable pattern for survival for all the other apps Apple "killed" today - you can still compete for any users that don't live 100% in the Apple ecosystem.