I have looked around the patch for gnome-terminal from Kristian Høgsberg and also the one for Terminal from Benny, and I managed to do the same for Terminal again since the vte libs have been modified, and support for real-transparency has been added. It was really simple, just init the rgba colormap, and call vte_terminal_set_opacity :) It requires version 0.13.3 or higher of vte.
Now someone could come with a good solution to integrate this nicely in Terminal. I think about a hidden option in ~/.config/Terminal/terminalrc, or even a slider.
Here is a first patch. It sets a hard-coded color for the alpha channel (0xDDDD).
Edit: And here comes a second patch which adds a hidden option for the opacity (ColorOpacity). It has to be in decimal, where 0xCCCC is 52428. Don't apply it over the first patch.
Edit 2: Benny commited changes to the trunk with support for real transparency, and a check for the version of libvte.