So you are very worried, that the Great Filter is in the somewhat near future of humankind.
But in the link you gave [1], the author personally thinks [2] that the Great Filter is probably in our past, in the evolution of higher life forms and intelligence.
[1] http://hanson.gmu.edu/greatfilter.html
[2] "I personally think that most of the Great Filter is most likely to be explained by the steps I think we understand the least about: the steps in the biological evolution of life and intelligence"
Bad things could happen if we over-estimate significant events, just as much as if we under-estimate.
Sure, it's highly unlikely. But imagine the profound tragedy that our self-extinction would mean.
Lots of stuff apparently.
What if a species communicates using pheromones and checks for specific smells similar to their own as in this strip http://xkcd.com/638/
What if there are creatures that live millennia and take days to form cohesive words.
What if the creatures are able to use physics that is unknown to us or that we can't detect?
http://www2.lbl.gov/abc/wallchart/teachersguide/pdf/Chap05.p...
What does the possible variation in life forms have to do with the nature of communications mediums or techniques? Encoding might be different but the mediums used will depend on level of technological advancement and not the specifics of how the life forms communicate face to face. (That's speciesist. I meant lifeform-to-lifeform.)
I love that KSR mentions Banks' Culture novels.
While I'd agree that biosphere sustainability is critical, I don't think it's the only critical problem, or even the most short-term problem, we may have. I may be paranoid, but I'm very worried that there is a Great Filter[1], and that it is some sort of abuse/misuse/weaponization of biotech at, or just beyond, our current level of technology. Just past that would be concern about unfriendly AI.
There are also some existential threats to modern advanced civilization due to low-probability but unmanageable-if-they-occur problems. Other than an asteroid we can't detect in time, there are also supervolcano eruptions that decimate world food supplies (volcanic winter).[2]
[1] http://hanson.gmu.edu/greatfilter.html http://en.wikipedia.org/wiki/Great_Filter
[2] http://en.wikipedia.org/wiki/Supervolcano