Software quality, documentation, testing is tedious and non-sexy for the most part. Because contributors to free software projects don't have to behave like customer facing pros they, for the most part, don't and you end up with poor UIs, non existent documentation and inadequate testing. The few exceptions (like GCC) merely underline how shoddy and amateurish much of the rest is.
So in a definitional sense they may be orthogonal issues, in a practical sense they most certainly are not.
Some free software is part of a commercial product, and is usually very well documented and reliable. Think WebKit, Firefox, Rails, and Google's many open source contributions.
Yes, and that just reinforces what I said. Free software done by pros is, mostly, done to professional standards, that done by amateurs is mostly done to amateurish standards.
What defines a professional or amateur, though? If you define a professional as someone that contributes to software as part of their paid work (and an amateur as anyone else), then Linux and GCC were both begun by amateurs, and are now maintained partly by professionals. Likewise, many projects are begun by professionals and receive contributions from amateurs.
That depends on whether you consider freedom in itself to be a quality or not, and if you do, how much weight you give to the freedom quality.
Then, the question is whether a certain proprietary software as enough other qualities to make up for the missing quality of freedom.
Also, freedom is not a pure ethical quality. It means greater independence as well as freedom of action, which both can be very valuable (in dollars), for companies even more then for single users.
So in a definitional sense they may be orthogonal issues, in a practical sense they most certainly are not.