Using robots.txt is the only way I know of to block the search engines from indexing certain areas or folders of your site. You can block at the directory level though, so you only need to tell the robots.txt file to ignore
www.mainsite.com/addonsite1.com/ and that should fix it for the whole addon site.
I'd also look into how the
www.mainsite.com/addonsite1.com/ is getting crawled in the first place as that shouldn't happen with addon domains. Are you submitting a sitemap from mainsite.com that includes those subfolders?