Thanks for helping and keeping us safe, but I'm sure all bots will defiantly come up as false positives on lots of these scanners.
As a general rule of thumb:
Normally if a botting website has an active forum, it's legit.
Plus you can read though script threads and see if the scrips are actually downloaded and working for people, if it is, it's most likely legit.
No one would take the time to write a 100% functioning bot and then use it to hack people, they would make much more money selling it vs hacking people.
As long as you're not using bots that are a file someone wants to send you over skype, but they're actually a well known bot with a decent forum backing it, you should be safe. I'm pretty sure that they would be able to mask virus' anyways, they're not that dumb.