From what I understand of this issue, the root cause is that AutoCAD produces actual dots at those locations– is that correct? If so, it’s not really an issue with Inkscape or what it’s doing, but with how AutoCAD creates the files. Does AutoCAD have export options that control these types of things?
In any case, you might be able to open up the SVG document in a text editor and see if there is any kind of characteristic that these dots have in their code– perhaps there is a way to identify the offending nodes and remove them programatically. I haven’t seen a file like this, so I don’t know what I’d be looking for.