I think someone already mentioned that the class of airspace is determined by the type and the amount of traffic in the area, not "what's routinely done". As for what's routinely done that can be covered in general in the beginning of the 7110.65 (in the US airspace system anyway).
Chapter 2. General Control 2-1-1
The primary purpose of the ATC system is to prevent a collision between aircraft operating in the system...
I know that's a very general instruction and it's starting to sound like this has happened several times to you. Perhaps you can call the tower and ask what you can do to help alleviate the potential conflicts while transiting their "D".
Civil courts don't seem to care official accident reports and lawyers only care about the parts that help get them more money. Once the lawyers get involved everyone gets sued from the FAA to the flight school who trained the pilots. Often the controller is only person directly involved left alive making their testimony very desirable. If the accident involves a small regional jet with 50 people there's potentially hundreds of different court cases.
There's a case where two VFR planes on sight seeing flights crashed into each other (I believe everyone died). The family of one of the people on board sued a 3rd plane having a gear problem,
and won, for talking too much on frequency. While it doesn't directly relate to what we are talking about. I bring it up to point out the technical rules of aviation like "see and avoid" or "no separation to vfr's in class D" have little bearing in a civil court proceeding.