A bit one sided maybe?
If Greenpeace was the only lobbyist she annoyed then she wasnt doing her job, given the lack of background to the article I'm taking it with a hefty pinch of salt. Anyway here's a great article in the Guardian about the sterling work she was doing and hopes that she would carry on :
http://www.theguardian.com/science/political-science/2014/jun/23/evidence-based-union-a-new-alliance-for-science-advice-in-europe
and then later an article about why the role is being questioned:
http://www.theguardian.com/science/political-science/2014/aug/29/the-eu-needs-science-policy-but-does-that-mean-it-needs-a-chief-scientific-adviser
Seems like someones being cynical about the green lobby when its dwarfed by pretty much any other lobby group, the decisions made by the EU are pretty transparent at least compared to our Government that is. There's always going to be the scientific view about GM crops and the publics view, if a good proportion of the population don't want GM crops then politicians aren't going to alienate the voters without good reason (you'd hope).