I guess I just can't resist the opportunity to champion the uninformed, but since this seems more of an ideologically motivated linguistic quibble than a technical or scientific quandry, I'll take a shot at it. I don't really see a great deal of irony or ambiguity in the use of the word pollution in this context. It has a fairly well defined meaning, which seems to apply here with very little needed in the way of an analogical stretch.
It usually seems to mean a factor introduced from without to a functioning system in some vital degree of equilibrium, the effect of which is known to impair the system from best functioning, or unknown, but conceivably able to impair in this way.
And no, the functioning or lack thereof of one system or another is not a moral question. However, since we who make moral judgements, and empirical ones, not to mention aesthetic and half a hundred other kinds of assessments of the value of any given thing, and hope to be able to use them to guide our actions are ourselves "systems in vital equilibrium" with a more complex, overarching network of systems (this is what the wacko, ideologically tainted science of ecology is getting at, in soberer moments when it is distiguishable from neo-Druidism and drum circle addiction), there is a survival value to paying attention to how what we choose to do affects our life support systems.
Genetic Pollution. It just means that the life-forms created in the labs of Monsanto et al. are capable, like their naturally produced near kin, of transferring their (altered) genetic information to crops other farmers are growing anywhere nearby, through the natural mechanism of cross-pollination. So it becomes impossible, or increasingly near so, for anyone to preserve any alternative to GE crops. I have even heard that farmers who have never bought GE seed have been charged with copyright infringement, or whatever legal definition is used, from the fact that their crops contain the identifying genome abnormalities, beyond much reasonable doubt transferred from neighbor's fields. Maybe they're the ones who should be sueing.
Oxygen was the world's first pollutant. Yes, this is a truly privileged viewpoint to be able to see things from, free from any taint of emotional involvement or subjectivity. Anaerobic microbes were in no position to effectively fight the introduction of this pollutant to their environment, and it went so much the worse for them. Maybe if they'd gotten interested enough in the issue early on, they could have organized and tried to have an impact on these developments. Maybe not. But we have this ability, luckily. All that remains is to see whether we have any more tendency to use it than the simple, prokaryotic microbes whose lifestyle has been so compromised by one of the pollutants we need to survive.