In my opinion, they should use a similar system to dp2 where if any files are detected as modified, it warns the user not to continue.
So with smite, they could detect if any "UNAUTHORIZED" program on your own machine running, they alert you that you're posing yourself at risk, not to go further.
Or at best, at least issue a warning, not a permanent ban through an automated means.
Automated bans aren't all that bad though, often used of forums most of the times to blacklist spambots. Another good use of ban automation is to ban users who are trying to hjack the requests a game makes to a server. For example, a flash game posting a variable to a database to update the score. A honypot automation ban could be used to punish those who try to modify "fake" score requests to modify their score.
This Smite circumstance is just a textbook example of how not to issue automated bans.
[Decided to go and post this in reply to your thread on reddit, too]