Gathering and BG botting are high risk activities for a bot, so you need to weigh whether you are willing to accept getting your main account banned vs. your want to gather/BG bot. There are definitely ways to lessen the risk. When gathering, I wouldn't gather for long periods of time in one zone. I would consider switching zones for short bursts of gathering. I'm not a BG botter, so I couldn't tell you how to help look less bottish there. From everything I read, the bot follows pre-mapped routes, so if someone knows the route you're taking, then you're easily identified as a bot by the haters out there.
I bot with my main account only, but it's only been to gather, quest/daily, and lazyraider in dungeons and raids. When gathering, I don't go for very long. There are others who bot almost 24/7 and still never get banned, so it really is luck of the draw most of the time. It'll always hang over your head. There will always be a chance you could get banned the next day.