If we can make a high resolution record of what happens in their brain when they report qualia, we can look at what kind of computation those qualia are, and therefore determine if other agents have them too.

I'm confused...you seem to be suggesting that we use behavioral output to determine which parts of the brain are responsible for qualia, which you say should define morality... didn't you just tell me that I shouldn't use behavioral output to define my morality?

If we did it the way you said, and looked at the brain to see what happened when people reported perceiving things, we'd find out some cool things about human perception. However, there's no guarantee that other minds will use the computation. That's why I'm emphasizing that it's important to focus on the input-output functions of the algorithm, rather than the content of the algorithm itself. (Again, this does not mean we ignore the algorithm altogether - it means that we look at the algorithm with respect to what it would output for a given input - so we still care about paralyzed people, brains in vats, etc...since we can make guesses as to what they would output given minor changes to the situation.).

(Not to mention, there is a cascade of things happening from the moment your eyes perceive red to the moment your mouth outputs "Yeah, that's red" and looking at an actual brain will tell you nothing about which part of the computation gets the "qualia" designation. At best, you'll find some central hubs which handle information from many parts. Qualia, like free will, is a philosophical question - all the neuroscience knowledge in the world won't help answer it. Neuroscience might help eliminate some obviously wrong hypotheses, as it did with free will, but fundamentally this is a question that can and should be settled without neuroscience. )