If you haven't already, you might want to add (setq org-catch-invisible-edits 'smart) to your config. It will stop you from backspacing over anything invisible,

If you haven't already, you might want to add (setq org-catch-invisible-edits 'smart) to your config. It will stop you from backspacing over anything invisible, but I don't think it stops the issue of highlighting a region and deleting it. This was a problem I ran into early on while using Org, but a combination of this setting and Git helped solve it.