So, as Ms Khullar-Relph asks:
How do you write about an establishment objectively when they're paying for you?
First and foremost, as a scientist before I worked for my present employer (and probably in the future!), I have a reputation to protect. I may not be well-known even in the aerosol field in general (let alone climate research!), but there is a core group of very influential scientists (read: past advisors who write recommendation letters!) that will call out any hackery on my part. So I have to be very careful and impartial while writing up the research I do with my company's instruments.
Second, where-ever I have been listed as a first author or a co-author, my affiliation with The Company is prominently displayed, just as a professor's name is associated with her/his university or independent research lab. So it is easy for the reader to look out for any soft spots, as it were, in my portions of that article. This formalizes the first point.
The third part is not writing, but peer-reviewing others' manuscripts - part of the "community service" scientists do. Not many manuscripts have come my way that present a direct conflict of interest - just two come to mind, over the dozens I have reviewed over the past four years. In one instance, I told the editor of my position; s/he found an alternate, and I was not required. In the second, the editor knew me well enough, and knew that I was one of the few scientists who would be able to properly evaluate the manuscript - my sub-sub-field is not very big, and I am actually very good at what I do! The editor said my review met his/her expectations. (This is part of the first point - keeping up my reputation.)
Finally, there is presentation of my research at conferences - something integral to science these days. Only once have I been asked not present my talk - even though it had been approved by the technical committee. Apparently, the conference did not want any private company to present, as some take advantage of the opportunity to deliver a sales pitch. As my fellow scientists say, I make a horrible salesman, telling people both the good and the bad about my instruments - gotta preserve the hard-earned reputation!
Bottomline - all I have as a scientist, really, is my experience and my reputation. And without the latter, I won't get very far in this age of peer-review that drives not only publication (the life-blood of a scientist), but also funding (the real life-blood of a scientist!)