Everything you do on ffxi is logged, everything. They have IP addresses you log-in with from the moment you started and they can cross-reference that with other accounts that may have logged in with those same ips, they have all this data available to scan though.
If someone dupes and sends the money to another account, it is all logged and they can trace it. If you goto some random spot in the world and trade or use a bazaar to get it to another character that is logged. There is no way to send items or gil in a way that is not logged by the server, no matter how smart you think you are. When someone is banned they go back through the logs and try to trace where money and items go because they obviously do look for this and they are well used to doing it to handle RMT that do exactly what you're talking about as a business model. This isn't done at the same time as the initial ban btw, this is done over a course of time after the initial ban and is done by the special task force.
So you don't know what they did or did not already do at all and are being mad for some reason over your assumptions, with no facts to back up your anger.
Here is the thing, there was no bug to take advantage of. They were literally "hacking" (really low tier hacking, but hacking all the same) the server, there is no grey area here where you are just taking advantage of a bug.
As for rollbacks, they can't punish the entire server for the actions of a handful of people (rollbacks is doing just that, punishing everyone by taking all progress away from them)...unless the duration is a matter of days and even then they have to really judge if it's worth it or not.