There's also a semi-auto delete user script that doesn't use the API called so-long-reddit-thanks-for-all-the-fish.

You go to your comments page, click a button, and it performs the actions within the browser. Without any further interaction, you'll see the screen scroll to the bottom, click edit on the last comment, enter the text in the script (default is a link to the script, but you can change that to anything), click save, and move on to the next comment (pretty sure it can delete, too). For best results, use a neverending Reddit script and keep scrolling until there are no more pages loaded. Also, re-sort the comments by each option (top, newest, etc.) to check for any stragglers.

You can still use your browser, though I recommend keeping the task in it's own window (in case your browser or an addon unloads pages you haven't accessed in x minutes). If you do something that makes the browser lag a little, it can cause the script to miss a comment, so you might need to run it twice. I used this on one account and it worked flawlessly for several thousand comments and skipped ~10, or so.