It seems this has not been done before, and upon initial investigation, I can see why. Many of the HTC Sense applications share common resources (themes, styles, icons, etc), stored in com.htc.resources.apk. So, if you attempt to modify something used by Mms.apk, but stored in com.htc.resources.apk, you are going to unwittingly modify the appearance of other applications, and if other corresponding elements are not adjusted in those applications as well, you are going to have problems.
So, things that are "challenging" are the things I like to try and tackle, and inverting this application was a tough cookie, requiring extensive edits, in some cases to "undo" references to items stored / defined in com.htc.resources.apk, and rather, make them stand alone directly within Mms.apk. This required major edits to XML, Styles, Colors, local .pngs, and Smali/Java code. You wouldn't think simply themeing an app would require all of this, but Mms.apk did.
Essentially, what this mod has done, for the most part, is flip most text that was black, and made it white, and most backgrounds that were white, and made them black (inverted), giving you a bit more visual interest, as opposed to the stock "white" look.
For those running a dark theme on their phone, who prefer to use the stock messaging app (I use Handcent, lol), this should fit the bill nicely. Again, thanks to Koni-man for the "nudge" / "coaxing" to take a look at this.
Flash the attached (HtcMms.zip) via recovery. Also, let me know if I missed anything. It is certainly possible, as there are so many menu options / tasks that can be done, that I may have overlooked.
EDIT: MetaMorphs attachments added (morph_*.zip), to modify the default 'tap to compose' area from gray (shown in screen caps above), to black (screen capture), and another to return the application icon in the app drawer to stock color. DO NOT ATTEMPT to flash these. They must be applied using MetaMorph, AFTER you FIRST flash from recovery the original mod (HtcMms.zip). After applying using MetaMorph, you will need to, at a minimum, issue a Hot Restart, for the application to re-appear in the app drawer. It will disappear after applying the MetaMorph, and re-appear after a restart.