You may or may not agree with me on this, but I think more people have flown their airmanship into the ground than their checklists into the ground. Not to say that you can't fly a checklist into the ground, because people have, and will do so in the future, but the emergency procedure memory items and checklists are written by folks who have the presence of mind to consider the best course of action for your given operation.
Now if it's obvious that running that checklist will get you killed, then by all means, don't run the checklist, but let's also talk about how often that's going to happen.
Don't get me wrong, I love to "what if" situations to death, but the majority of the time this stuff is going to be cut and dried stuff, and the emergency procedure checklist is there to mitigate pilots from creating their own procedures when they are, quite literally, on fire.
Its all a matter of timing. No one is saying don't run a checklist or toss it aside. It's simply a matter of when to run it. You can't simply rely on one or the other regards airmanship and checklist usage, you need both. But there is a time for each, and even a time to use both at the same time. When those times are will likely be different for each and every unique emergency. But the two do complement each other.