If you want thunderbird to compose emails in plain-text format by default, you can edit the file mailnews.js. To find this file, go in the directory where thunderbird is installed, and then go to defaults/pref/.
Open the file, and find the line
pref("mail.identity.default.compose_html", true);
Change it to
pref("mail.identity.default.compose_html", false);
Restart thunderbird.
Maybe one day it will be possible to specify this through the preferences panel...