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.