I'm not the techie, I'm just the... techie. Whatever, I don't work on the Blender Source Tools, I just know how they work, so don't ask me. Either way, don't expect it.

But one way it could possibly be done, Artfunkle/Artfunkel/the author of the Blender Source Tools, would be I think to first import the mesh with its armature separate from the already existing armature, then loading the position and rotation data from the existing armature (like when importing an animation) and applying it to the new armature, then moving the mesh over to use the existing armature as skeleton, and deleting the new armature.
That would just cause problems when there's more than 1 armature already...
Well, it's a possibility, I think.

This is because the Blender Source Tools import the reference mesh of SMDs and DMX', not taking their bone positions into account, as that could produce rather strange results, depending on the already existing armature.

Oh, Source supports vertex animation. It's called "shape keys" or "flexes" in Source, though.

Check your .smd files in something like Notepad++. There should be a lot (lot) of lines if it's something other than a cube. Or zoom out or something. Source Engine files are a lot bigger than Blender cubes and such.

Yep. Fixed.

I honestly don't know what to call this bug, so I decided to not call it anything.
Anyways, using Blender 2.69 on a 64-bit Windows 7, I can't export .dmx animations with version 2.0.2 of the Blender Source Tools (only tested with one single one-frame animation, though).
As I'm not a Python-loving guy, I can't make sense out of the error[sta.sh].
I can't upload relevant .dmx file(s) (unable to export them) nor .blend file (I don't save projects for small things I expect to finish quickly).

...Oh, so there is actually theoretically an armature when importing "boneless" meshes. Alrighty then. I feel like I'm submitting a lot of bug reports. Thank you.

Well, it may just be because I'm using the awesome .dmx format (bare with me, I'm drunk), but whatever.

I can import sourcesdk_content/tf/modelsrc/player/[class]/dmx/* Level-of-Detail meshes just fine, but if that's all I do, the chance of me being unable to export it afterwards (without adding an Armature) is quite big, since, because of the fact StudioMDL is able to auto-assign vertices to boneweights by matching their position according to the lowest/standard/default Level-of-Detail, VALVe's Level-of-Detail meshes don't contain bone data, and Blender complains when trying to export meshes without bones or something.

Currently, that makes me stuck on a Scout playermodel skin I'm trying to make (since I'm just too lazy to do it the unbelievably hard way).

Using Blender 2.69, Source Tools 2.0.1, 64-Bit Windows 7.

Well, that's good to know, I suppose. Thank you.

http://sta.sh/0mzk6h0nxtb
An uncompressed .zip file (no, really, it is actually uncompressed) filling about 7 MegaBytes, (hopefully) containing all files related to the model (except textures and actual compile) that I am comfortable with giving out. If something is missing, let me know.
(Head.dmx is probably only compatible with the FilmMaker's StudioMDL, unless imported and exported to a different "Engine".)