No, your main should be fine as long as you're just botting one or two alts. I use to have two tanning bots going while I was on my main.
If you have a huge farm going on the same IP as your main, you may get chain banned.
Keep in mind though that nothing is definitive, and if you want to have the lowest possible chance of getting a chain ban, use a proxy on the alt. @Token has nice, cheap proxies.