Hello, I have a similar problem, but I already have my Checkout set to false. I can still successfully place orders for items that I have marked as 0 quantity in the Stock by Attributes area (Catalog > Products with Attributes Stock). I have tried both deleting the zero-quantity listings and just typing "0" in for quantity and it seems to not make a difference. Here are my current settings for the admin > config > stock area:
Check stock level true
Subtract stock true
Allow Checkout false
Mark product out of stock ***
Stock Re-order level 5
Show available stock level in cart when less than order true
Display Images in Admin false
Products status in Catalog when out of stock should be set to 1
Show Sold Out Image in place of Add to Cart 1
Product Quantity Decimals 0
Show Shopping Cart - Delete Checkboxes or Delete Button 3
Show Shopping Cart - Update Cart Button Location 3
Show New Products on empty Shopping Cart Page 1
Show Featured Products on empty Shopping Cart Page 2
Show Special Products on empty Shopping Cart Page 3
Show Upcoming Products on empty Shopping Cart Page 4
Show Notice of Combining Shopping Cart on Login 1