The only real solution is allowing people to deplane from both the front and back doors. I know they do this with the DCA - LGA shuttle flights (at least they used to when I flew them frequently a couple years back).

I do agree this is a problem - especially with airlines scheduling increasingly tight connections where you can either (a) pay for a C+/E+/MCE seat (if non-elite) to get off more quickly (b) risk the connection or (c) be forced to take a much longer connection to play it safe