If I understand correctly, you'd like firefox to open tabs in the background and not be pulled to the top with focus from an external program URL request.
I don't know the answer, but found this http://lifehacker.com/263940/force-l...the-background which might help.
When I did a man firefox there wasn't a clear command line option to prevent raising the window. That would probably be dependent on your window manager and focus settings. Openbox is what LXDE uses, this page https://help.ubuntu.com/community/Openbox explains some of the options.
I found an openbox guide that showed configuration settings like these:
The layer might be important, though the maximized=yes is just scary.
It appears to be that your window manager and DE will determine how this behaves.
Another idea is to place the Firefox program onto a different virtual desktop from thunderbird. When I client a link in thunderbird, what firefox does isn't seen (FF opens the link inside a new tab) so I'm not distracted. I tested it and it does work.