Maybe the college rule that DPI is an exception to half-the-distance is a remainder of this old rule.
I agree that eliminating half the distance would discourage penalties in situations where the full yardage can be enforced. Putting the ball at the 1 (or at the 2-yard line, for DPI in NCAA rules) is fair, because it gives the offense an opportunity to be in scoring range, especially when a foul was committed to take away a scoring opportunity.
Another potential solution to fouls that take away a scoring opportunity in half-the-distance territory is to make all personal fouls, unsportsmanlike conduct by B, and DPI carry an automatic 1st down. This would also deter unsportsmanlike conduct and unnecessarily rough play by B in situations where A has to face long yardage, where the penalty might otherwise not affect anything for B (a sack makes it 3rd and 20, but B57 flexes in the face of the downed QB).