What you could do - instead of making it a subfolder of Assets, make a folder on the same level as Assets. Unity will ignore it, and you can add it to Subversion so it's sync'ed.

This is a totally sketchy hack I am currently testing out now that allows you to use the unity3d branded asset server with c# files that are not supposed to be intrepreted by the unity engine.

1) create a local svn repository inside of your asset folder.

2) check it out to the folder on the same level as assets

3) Add ignore tag to asset folder and library

Now you can add files outside of the asset folder to the local svn. Then When you check in the Unity3d project to the asset server, the local svn gets checked in.

Basically, it adds a level of indirection...

Perhaps the simplest option - make a project just for the DLL? That way it should compile fine in unity as source, and you won't need to keep the DLL in the project

If you're using SVN, you may be able to add an svn:ignore tag to the files and/or folders that you don't want to be synced, though I'm not sure if Unity Asset Server respects that property or not. Other than that, I'm not sure (and my guess is it's not possible).