This is what I do:
1. Put this scripte somewhere and make it executable:
# This script allows external apps to open new URLs in Firefox
# or open a new instance of Firefox if it isn't already started
/usr/bin/firefox -a firefox -remote "openURL($@,new-tab)" ||
exec /usr/bin/firefox "$@";
2. Add the following lines to your ~/.thunderbird/default/prefs.js file:
Make sure you do the above when you are not running Thunderbird.
Note: I didn't write the script, but I couldn't find the link.