"Qualia" means what we subjectively experience. Calling them qualia doesn't have any particular implications. It's just a name for what everyone reading this experiences. If that experience rules out certain analyses of how consciousness works, then it's bad science to discard the data.
If we say that the sentence "what we subjectively experience" is valid at the level of the whole organism, what do think it looks like if we examine it in terms of brain processes? Where is the "we" and where is the "experience?"
Nick