It should also be noted that Maplestory should not be trying to run a monopoly on people's computers. I'm not sure how deep the detection program goes, but simply having stuff installed that is not running while Maplestory is should not trigger a ban (if that's the case here).
As mentioned on the Reddit post, some people have various programs installed for school and work. Things like AHK are legal in other games to do specific functions that those Devs have deemed OK. Most people using a controller in any of the games they play from PC will likely be using some kind of software to play.
This doesn't even begin to touch on kids that use a family computer and don't have the technical know-how or permission to kill idle processes their family members may use regularly.
Surely you can see how this can get out of hand quickly? I appreciate everything being done to rid of us hackers, but honest players should never be permanently banned in the process.