Because it took me awhile to find this, I want to document it here. You can change much of the preferences in Thunderbird through the GUI. And you can change them directly with the Edit -> Preferences -> Advanced -> General -> Config Editor. But there doesn’t seem to be a way to set the color of the cited text in a plain text reply. In order to change that, you have to edit/create this file:

/home/[username]/.mozilla-thunderbird/[profile].default/chrome/userContent.css

In that file, place the following CSS clause:

span[_moz_quote=true] {
color: pink ! important;
}

But shut Thunderbird down before you edit that file. Thanks to this forum thread for the answer.