Those Boxer fans who are equating the introduction of the original K-Series and BMW's desire to drop the Boxer with the current situation are missing two important factors:
In the early 80's, it was simply a desire to drop the Boxer that was the spur for BMW (for a variety of reasons such as rationalisation of production and reduced R&D).
Now any decision regarding the Boxer's longevity is really in the hands of the EU legislators. The noise pollution requirements will kill the air-cooled Boxer. This won't be retro-active (as it wasn't with two-stroke), any engine in production at the time the new regulations are introduced will be permitted to remain in production but won't be allowed any major changes (I think that's the reason for the 2008 upgrades; get them in place now to extend the model life/maximise potential return on tooling etc.).
Also viz the situation when the K100 was launched:
BMW made no other bikes than Boxers. All their customer base were Boxer owners and BMW didn't have a large customer base that was switching to the new K-Series.
Today the situation is very different. BMW have sold singles, parallel-twins, K-Series "Bricks" and across-the-frame K's to people who have never owned (or desired) a Boxer.
There's a huge number of BMW owners out there to whom the Boxer is irrelevant.
BMW don't make bikes because they want to. They make them because it makes money. While they may maintain BMW "Tradition" for as long as possible, once it becomes financially problematic, they will have to change (as they have done with the K Bricks, F-Series, belt-drive, chain-drive: All things that were once contrary to BMW "Tradition").
They may find a way around the noise pollution with a water-cooled Boxer but I suggest that it will come down to a fine balance of economics. The question will be: Develop a Boxer that meets the restrictions or concentrate on the water-cooled models that they already sell in vast numbers?
As much as I'm a big fan of the Boxer, my money is on it being dropped. It is my guess that it will soldier on for a while, particularly in the GS and maybe the RT too.