I also think it is unfair if you're banned unjustly as that's certainly a given. However, there are more than 25,000 users daily playing this game. Not everyone uses programs for malicious intent or even at all, however it is very difficult for each staff member to keep track. If I'm not mistaken, there are less than 100 staff members in total. Not only that, out of these staff members, not all of them have the power to ban or detect bots. Let's say there's 100 staff members for the sake of it. Do you expect 100 people to keep track of all 25,000+ people? To be fair to them, they have their hands tied.
Their responses could be a bit better as I'd be extremely irritated if I was banned for the reason you've mentioned without any evidence, however the aforementioned must be taken into account - they've got 100 people working. They have lives as they aren't paid to be staff members. It is easy for you to be angry, and you have all the right to be, but you must understand that they are humans who do not get paid for this work. While your anger is justified, try to understand and be careful in the future.
Unbanning some people who may have been botting means that the botters will be more intelligent and find a way to bypass detection. They will not make the same mistake twice. I know this because I've been in staff positions for a few MMOs and this has happened a lot on. It is a high risk, no reward situation for the staff members and everyone involved. The bots will take over, ruin the economy and fun for players, give the staff members extra work to do that could have otherwise been avoided while new problems will arise. Give people an inch, they'll take a mile.
The situation is the same for ALL MMOs, not just this one. That's why the banning rules are quite identical.
Edit: I just wanted to say one last thing - be careful the next time any software is on your computer. Some applications start automatically upon logging in your computer, so do your best to close them before opening PokeMMO.