Is there any way to completely remove associations set for Modern UI apps in Windows 8 (like opening webpages, files, etc.)?
You can do this with the Set Default Programs option in the control panel.
To access this, press Win + W and enter Set Default Programs, now you can go through the programs and apps installed and use the Choose defaults for this program to enable and disable different default programs.
For example, you can set the mailto protocol to use Windows Live Mail (or another email client) by selecting it for the application you want.