Prevent Keychain from copying an internet password to the login keychain

Manually enter your username and password. Tap "Passwords" right above your keyboard. Tap "Save This Password." It still won't autofill when you first load the page, but now you can tap in the username field and hit "Autofill Password." There seems to be no way to actually reset the "Never for this site" setting. Sounds like a job for http://apple.com/feedback.

I hate to reference unreleased software, but quite frankly the solution may be for you to enroll now in the iOS 9 public beta or simply wait for it's official Fall release. iOS 9 (at least in its current state) gives the option to set a custom alphanumeric password in place of the familiar 4-digit pin.

So, if you have hardware with touch ID capability you could use that for your everyday login and reserve a more complex passcode (even the same as your iCloud one, like you mention) for protecting your keychain in case of theft, etc.