Seems odd to leave just as a new product is in beta stage...
Not at all...
The "betaness" of Lightroom 2.0 is merely the public beta which was locked down mid-March. Since then, internal testers have much later builds that are a lot more finished and the parts that Mark was involved with codewise are pretty much done (except for bugs–some of which Mark was working on literally just before going to his going away party).
This was a golden opportunity for Mark and the timing, from MSFT & Adobe's point of view was fine. Truth be told, Adobe was sad to see him leave–just as they are sad to see anybody who's been there a really long time and accomplished a lot–but there are plenty of talented people to carry on the work. The primary work Mark did (with code) was the develop pipeline and working with Thomas Knoll and Zalman Stern and new hire Eric Chan (who hangs around here as well). Thomas and Z are perfectly capable (and in fact did much of the code anyways).
Mark's vision is what produced Lightroom. He had worked on it since early 2003...five years. He got it launched as a beta series and then a final shipping product and now is leaving at near 2.0 release. Now WAS the time to leave. His vision is already in play and the direction of Lightroom has already been set.
Where's he's going, he'll be working on something entirely new–User Experience–and he won't necessarily even be writing code (Mark doesn't do Windows all that well, he's quite the Mac bigot), he'll be designing the environment of future OS's. Something that will be incredibly challenging and difficult–which is EXACTLY what he was looking for at this stage in his career.
There really wasn't much opportunity for Mark left at Adobe other than pure research. He had been in the ATG (Advanced Technology Group–where he developed what would become Lightroom) where some really smart guys at Adobe end up when there's no particular product they want to work on. But he wants to do cool stuff on shipping products, not just pure research.
He was done with Photoshop...he was done with Lightroom and he wanted something completely different. And where' he's going, it will be COMPLETELY DIFFERENT now because Mark is on the team...we who know him all wonder if MSFT really knows what they are getting :~)