Of course, there will necessarily be a split, but developers can still adapt MOS program to OS4 and OS4 programs to MOS easily. That'll change progressively, but this is the case ATM.
Personnally, I don't care if MorphOS is not the official AmigaOS ; if it's better, I'll stick with it :-) Anyway, AmigaOS4 does not share much more with the origial AmigaOS (as most had to be rewritten, as in MorphOS, and as it runs on completely different H/W, like MOS).
So for the moment, I prefer MOS because it's available for a long time, works well, if thought for the future with the boxes system, and because Genesi is much stronger than Hyperion/amigaInc, and make their own hardware. But if AmigaOS 4 turns out to be better and available soon, everything will get more complicated
I just fear people choose OS4 over MOS just because of the name. Anyway, OS4 should be available soon and we'll be up to compare the two systems objectively.