I have been playing free to play games more than enough to know what kind of situation there is there. Not Archeage, but other ones. However, I also know that it varies from game to game. And there is a reason for that. Some games are simply more attractive for botters than the others.
You're talking about the current item mall in terms of a possible free to play item mall...What makes you think it is a good idea?!
I'm 100% sure there will be a lot of stuff that players will want very much on a free to play item mall...that will be tradeable. The reason why most of that stuff is not is exactly to minimize the effect of buying your gil with real money. But once this game would turn to free to play I very much doubt that Square would care about that in the slightest. They'd pack it with consumables that are tradeable for players to buy, so as to monetize the non-paying consumers through the "whales" that would buy items explicitly for sale. That is only normal. That's a vast part of where income is in free to play games.
Because I know, just like Square Enix, that their "contract" won't hold water if someone will really push for it to court with a valid case. Agreements between two parties cannot supersede the law. They are a company. They cannot just ban people randomly for no reason on a whim, especially during the paid term.
Then there is the case of press release, and while Square Enix shows the middle finger to the community a lot, there is a major difference between not listening to requests and making poor design choices and making months of years of effort irrelevant for no reason.
A person that is being shafted by there being no particularly worthwhile content time and time again may still log in here or there to do the older one, and that means that will pay the sub here or there. If not, there is a chance of them returning after an expansion.
A person that is being told that they may lose all the effort they put into the game and start from scratch, even if they never did anything remotely dubious, will think twice whether he wants to actually invest in the game at all. It's one thing with free to play games, another thing entirely with sub games where you literally pay for nothing gameplay-wise.
Except the bots won't stop being made. If they leave the bots, they'll get a sub once a month. If they'll ban the bots every day, they'll get thirty subs in a month. Clearly it's better to ban them than not money-wise.