I disagree, it is at least in part Apple's fault. We sacrifice a fair bit of control because of Apple's closed iOS. At the end of the day the cookies are only pieces of data. Within the realms of the phone iOS there is absolutely no reason why that data cannot be deleted.
I'm not saying the data won't be written back if you visit that site again, but at the point Safari is closed and you request the data deleted it should actually be deleted.
If sites are using tricks to make this data persistent then Apple is a multi-billion dollar company that could easily rectify the issue, but at this time it would seem they simply choose not to.
Unfortunately despite being a potential privacy issue the problem seems very low down on Apple's to-do list as there have been multiple updates all of which have failed to address the issue.