Is there a keyboard shortcut in Mail.app for moving the active email to the top of the inbox?
It's annoying that there isn't a simple keyboard shortcut for this. I suggest providing Mail feedback to Apple if you'd like to see it work properly.

For a workaround, try the following AppleScript:

tell application "Mail"
    set the selected messages of message viewer 1 to {} -- deselect messages
    tell application "System Events"
        key code 115 -- scroll to top
    end tell
end tell


You can make this into a Service and assign a keyboard shortcut to it from the Keyboard section of System Preferences.