I think the issue here is just a matter of abstraction :) You claim that having files stored that way is a "problem". However, you haven't mentioned WHY you consider it as problem.
Just doing some guessing, your intention is to browse those directories. If that is the case, then that is the problem. That directory is not there to be browsed but rather to be internally and efficiently used by Q2A.
If you need to browse the blobs (which by the way, they are not just uploaded images in posts but also avatars), then you must use a higher level of abstraction to do so. You can do that by means of a plugin that fetches the required information from the core. In fact, that plugin wouldn't even care about how the blobs are stored as the Q2A core is smart enough to abstract the plugin from that.