I'm sorry that you lost your "main account." I know how attached I am to my main account, and it would be painful to lose it.
Blizzard has figured out tons of ways to detect botters, but not necessarily the buddy program. If they detected the buddy program, then we would all be shut down the same way Blizzard shut down everyone using WOWGlider a few years ago. Botting is a risk no matter which bot program we use. We may feel like it is a calculated risk, but we really don't know how painful it is to lose a favorite account until it happens.
So, I'm sorry for your loss but I don't think this necessarily means that the buddy program has been detected. It probably means that one of your toons did something bottish (just like all of our botted toons) and your luck ran out this time. Most likely you were reported.
I do agree with your comment that "no one is safe." But, I don't think anyone was ever "safe." It's a risk we chose to take.