That's certainly an option, although having the comments in context while you listen to the track is for me a hugely better workflow. There would be no way to see all the comments for any given track easily and they would also be difficult to associate with a particular part of the track.
So - yes, could be done, but I think it would be a big step backwards!
The simplest 'solution' is that if you don't want to pay for SoundCloud (which I completely understand) then you just delete / move old tracks to make room for new OSC tracks, as other's have said. There will always be some limit to storage on a free service I imagine!