My situation is indeed different to yours. However, a professor sometimes
have to face ethical issues too: for instance, using didactic material that
is not free (I have to do that this semester because I was asked to teach a
basic course based on a common textbook, with common exams and taught by five
other professors... including the author of the textbook), partnering with
companies that want the academic developments to be under their copyright (I
have always refused such a deal), signing copyright forms for the journals
where the research is published (anyway, I make all my articles freely
accessible from my website), using Windows rooms when they are the only ones
available (what I taught at that time technically required the GNU tools and
I made the student work over SSH on GNU/Linux systems), etc.
Lobbying (what includes entering some decision bodies) is a key to make the
university a more ethical place. Not everything can change overnight and a
transition period is unavoidable. Notice that rms does not pretend otherwise.
He says that universities should only use free software and need to plan a
transition over several years to do so (otherwise it would be a failure and
no university would ever switch to free software).
I am also in favor of small businesses. Large corporation have far too much
political power nowadays. I would even say this is the greatest problem the
occidental world is facing: they are turned into "corporocraties" and
(focusing on IT-related problems) vote laws such as ACTA, SOPA, PIPA, Hadopi,
etc.
Again, nobody tells you to violate the contract you sign with your customer.
It should clearly state that you will work in an ethical way, hence produce
free software.