We wanted to secure ArcGIS Server using database credentials so we developed a custom ASP.NET security provider.
We also wanted to secure our website so we implemented ASP.NET forms authentication using the same security provider. This website is one which generates tokens and all entire ArcGIS Server system lives behind the firewall. We do not hand out tokens.
We also provide our own REST endpoints via the website but getting that to work with ASP.NET forms authentication was tricky, i.e. there is no interactive user. In hindsight, I think that we should have implemented custom basic authentication.
Security is a deep subject and I am doubtful that you will find simple or easy answers. You will need to roll up your shirt sleeves and dig in!