What does 'Delete' do?

Hmm, it appears you are right. We should rename the operation. I agree that "disable" is a more appropriate name.
About checkboxes: BOTCHA protection management is not so simple to just turn it on or off. There are many recipe books that could be enabled one per a form. That's why we have "edit" operation near each form: you can choose which recipe book to apply to a form. Let's think what is 'disabling' in that case? In my view we have 2 options:

• either create a fake recipe book 'none', which purpose is to provide a unified way for disabling: each disabled form becomes protected by 'none' recipe book;
• or (as you have already mentioned) add on/off checkbox: the protection for a form could be disabled without touching related recipe book.

I tend to agree with you again: the best way is to add an additional checkbox.
Let me think about it for a while.

If you go the checkbox (or even tableselect) route, you might want to consider using drop-down select elements for selecting the recipe books, rather than separate 'edit' pages that do almost nothing but require many clicks and page loads. A big fat [Save] button at the bottom would allow to update all forms at once.

That is how it was done earlier. I have refactored this implementation replacing drop-down select with edit links. I understand that this solution is less user-friendly - but here is my argumentation: for admin links functionality we need a way to edit each form separately. So in the old version there were 2 independent ways of editing the form: via common page with drop-down select and with the help of individual page. I don't like this situation because it doubles the efforts needed for maintaining this stuff. So I have unified the interface making it easier to maintain to the prejudice of usability, sorry.

Just to voice my opinion:

The usability regression such as removal of drop-down lists is well substantiated for the sake of moving the massive rewrite forward quickly.

Once the redesign is complete however, I think we should restore this functionality. Having a "none" item on the options list (in both places - edit form and forms list) is the most convenient way to quickly unprotect a form without removing it from the database and keeping the schema simple.

This approach serves a secondary purpose - keeping a list of important forms and decisions that were made on their protection strategy.

Further improvement could be to show other protection modules' settings (Captcha, mollom) for the forms in one place, allowing the admin to easily design a comprehensive protection strategy. I can explain how I see this will support the high-level strategy for Botcha project development, but it is venturing outside of scope for this issue.

I understand. Too bad...

Don't worry, everything is under control!:)
Looks like fixed by commit for #1840702: Create a variable which lets (or not) to edit the list of forbidden forms and provide an UI for editing it (see http://drupal.org/node/1840702#comment-6736118 for details).
Enjoy!