IP isn't the only kind of value. MakerBot has a pouplar hardware product in active production, which represents a pretty big investment that can't be easily reproduced (or Stratasys, which makes its own hardware, would probably done so). They have a very strong brand, including the Thingiverse site. These are things that drive Replicator sales in the future. And Stratasys (correctly) views them as someone they'd rather acquire now than in three years.

That said: yes, the MakerBot really is just a refined RepRap. There's not much really of unique value there, technologically, beyond the aforementioned high expense of "refining" a hardware product.