Q1: What happens when you dive charge a creature from straight above? Do you end up landed in the creature's area? Do you smash into the ground?
A1: I believe this is covered by the article you linked "Colliding with a Creature" as well as http://www.d20srd.org/srd/combat/movementPositionAndDistance.htm.
Accidentally Ending Movement in an Illegal Space:
Sometimes a character ends its movement while moving through a space where it’s not allowed to stop. When that happens, put your miniature in the last legal position you occupied, or the closest legal position, if there’s a legal position that’s closer.
In summary, I believe you would collide with the creature but then it depends on that creatures size what happens. The article reads you must overrun unless they cannot be overrun then it gives suggestions. As a judge, I would be inclined not to give any additional bonuses to your overrun (like for example Improved Overrun) since you used your "attack" to charge, unless you could provide documentation strongly suggesting the contrary (otherwise in my view, you'd get "two attacks" which is rules bending). Regardless you can't break the occupying rules here so would move your figure to a legal square if you're left in an illegally occupying position per the SRD quote. Since you must continue falling, it would be land square adjacent to the target (not hovering:P) then you'd strike the ground.
Interesting to note, they say those rules arn't official and are suggestions but it comes from WotC so not sure what they're trying to say there.
Q2: If you have the diving charge feat that allows you to "turn so that you are parallel to the ground after the charge", could you automatically recover from a freefall by doing a diving charge?
A2: I would rule that you have not spent a full round to break the free fall so would continue to free fall. That's definately a greyish area but it sounds like (I did not check the verbage of the feat, just went with your quote) the feat affects things disjoint from the falling (affects charge, not affects freefall).