Old post, but still relevant...
I don't know if you can, or should replace it, but you could write an overlaying app to cover it and do it's own thing, if you can use a little windows command-line magic combined with node.js. More of a work-around, but then you won't chance destroying any os-specific functionality, and it seems to be universal from Vista on up (to my knowledge at least). Here is how you can get your starting point to run a GUI app on the logon screen.
Node-Windows - Run GUI app on Logon screen
You can use this technique to run any app in any language that you can open it's window from a command-line.
There will be a brief period where the normal logon screen will be visible before your app starts, but this will let you do it.
Whatever language you use for your logon GUI, you will need to send simulated key input to the real logon screen, possibly mouse-clicks-- but you can likely use simulated tabs to get to the right logon. Likely MS has API's for C# as well as a variety of related dialects to programmatically logon to the desktop in a more elegant fashion than this last part, however.
Your app will be running as the SYSTEM user (unless you specify otherwise), therefore it will be running with the highest authority-- so you can basically do anything that is possible from there. Permissions won't stop you. Be careful with this.