What you do there is storing data in "the cloud", thus you give control over
your data to someone else, which is a bad concept of security and privacy.
You should store everything locally and only access servers for looking at
websites, not storing your personal data there.
However, if you really need to store stuff online and there is no other
option for you except setting up a private server to do the same thing, use
Spideroak as before (or setup a private server for the same thing obviously).
It doesn't really matter what software the spideroak server runs, as long you
as you can access and use it with your free software. There is no moral
issue, at all.
There is only a moral issue if you have to use a computer set up for your
personal use, a computer where you are supposed to be able to install/remove
software. Then you are "obligated" to install a free OS and only free
software on top, but there is no such obligation with servers. You aren't
supposed to install software there, so the moral issue is only with the
company who runs the server, not with you.
If you wanted to access a webserver that has Windows Server running on it,
you wouldn't object to that fact either. One may hope for the sake of the
people who run the site that they install a GNU/Linux on their machine, but
it's their business, not ours ;)
