> Warning when a site doesn't use TLS is a clear cut case of crying wolf.

No, it's a warning sign that you may be an active victim of an HTTPS downgrade attack where an attacker is blocking HTTPS communication and presenting you with an HTTP version of the website that you intended to visit, capturing and modifying any information you transmit and receive.

> By throwing scary warnings in front of users when there is no actual security threat

Most of these situations may be innocent but the problem is that they look identical to "actual security threats" so you don't have a choice. If there was a way to distinguish between them we/they would be doing it already.