It is of course totally up to you.
Rate them how you feel or you could soften it and tell them everything in the private feed back. They aren't going to know unless someone tells them. If it was dirty, there is no excuse for that. Organized kitchen is subjective to each persons taste I suppose.
The other things you noted should be noted to them. You don't have to be mean. I think one of the choices is cleanliness. You can rate a 4 and use the private feed back if you want to give them a break.