Linux is not against anything, much less against you paying for the software you use (in fact, there are commercial Linux distributions just like Red Hat).
If you have a thousand million files on a proprietary format you can't blame Linux for not being able to open them. It's like buying a thousand games for psp and then blaming your nintendo ds because it can't play them.
People should really be more concerned about proprietary vs. open data formats. That, and only that
, is which decides who is the true proprietary of your data.
I can only give you two suggestions: either try to work closely with the wine team to get the publisher support into shape or research in the internet for a way to convert the pub files to something else that doesn't tie you to MS.
The place to start with the former is this:
The place to start with the later is this: