I'm not convinced about the dismissal of option 2. I agree ST is clunky but not for the reasons given. It's clunky because it's impossible to mix with other effects. What if I want ST and exceptions, for example, and I want the presence of both to be tracked in the type signature? ST can't do that. But my effect system, Bluefin, can. In fact it can mix not only state references and exceptions, but arbitrary other effects such as streams and IO.
* https://hackage.haskell.org/package/bluefin-0.0.2.0/docs/Blu...
* https://hackage.haskell.org/package/bluefin-0.0.6.0/docs/Blu...