No, SidePosts didn't ruined your DB! SidePosts is working fine with WordPress 2.8.2. I think you're using the last version of the plugin.
The plugin does not write to the database (except for its own settings) and dows not change anything on the posts. So, your database should be Ok what to this plugin is related.
Perhaps you got a failed install, a failed WordPress update or a failed plugin DB. If you removed the plugin and still getting software failure notices, you have to look for the problem in another side.
I would make a fresh install of WordPress and plugins (Checking requirements and compatibilities of all). Probably this would solve your software failures.