Why can't SE just ban the bots?
Because from what i've read they currently don't have that special team working on finding out who is botting. And I'm assuming it would be very difficult to mass ban people in the future based on recorded data without banning a number of innocent players. So its very likely those who have botted to this point have gotten away with it.
This thread is long and I did't read it all. I may have a solution.

1) Let the players the ability to flag someone as being a botter

2) If someone is flagged as a botter and is engaged in a combat (or gathering, crafting), nothing happens until the end of the combat. When it is time to reap the benefits (exp, items, gil, etc) the game delays the rewards until the suspected botter correctly answers a question. A picture is then submitted to the screen with fuzzy text (just like when you create a new hotmail account). If the suspected botter type the text right (could add voice to help), he (and his party) can have all the rewards. After 3 tries the botter account is locked for review by SE and no reward is granted.

3) If someone is flagged as a botter and is not engaged in a combat (or gathering, crafting), nothing happens until a combat is engaged. Then proceed to point 2.

If you like this idea please click "Like".