Deleting own comments is rate-limited to one every 5s, similar to voting on comments... not good. An example scenario is a Comment thread where you were talking with someone who deleted their Comments (for whatever reason), rendering yours no-longer-useful.
I recommend looking at The Complete Rate Limiting Guide.
The assumption is that if the UI does not allow you to do something that you need rarely, and that is severely hindered by rate limiting, you can ask a moderator to do it via a flag. This is a correct use of flagging, even if you are flagging your own content. The moderator's role in this case is to apply common sense to see whether the mass deletion of comments is something that will leave the site better off, while respecting your rightful wish to delete your comments. The moderator may take additional actions as he sees fit as well, depending on what kind of content is being mass-deleted.