By the rules, one simply cannot Overrun as part of a Charge.
I agree with previous poster's assessments that this was done to 'protect' back row types from unfriendly attentions. However, I am not sympathetic. Lots of solid tactictal options are available to defending mooks: ALL Overruns provoke AOOs, weapons can be set to recieve Charge, and Readied Actions can allow additional defenders to intercept a charge (moving to where an AOO is provoked and/or the overrun can be opposed).
What I've done in my campaign ('Bahwoooga!' - House Rule Alert - 'Bahwoooga!') is change Overrun from a 'special Standard Action' to a 'Not-an-Action'. It is simply an event that may or may not occur during Movement. If, during movement, a combatant attempts to move through a square occupied by an opponent, we resolve it as an Overrun.
This allows combatants to blow through opponents as part of a Charge or as part of normal movement. Of course, if the opponent succesfully blocks, the rest of the Charge or Move action is lost.
It hasn't come up too often, but the players seem reasonably happy with it.
One thing I'm not 100% clear on is if a Readied action (which only allows a Standard Action) counts as 'If you are able to take only a standard action ... you can still charge". Because if so, defenders could even Ready Actions to Charge a Charging attacker (only moving 1x movement).
A'Mal