It does seem a strange decision. They even address it in their post:
"jQuery was conceived specifically to address the differences in browsers, so we’re not going to abandon the essence of our philosophy and simply disregard the millions [still using] oldIE. Yet we also want to move ahead and take advantage of modern browsers, especially the growing mobile market."
The whole point of jQuery is that it's supposed to allow you to move ahead without losing backwards compatibility. Making this split -- especially with a version number, which implies a feature-freeze for 1.9 and new stuff only in 2.0 -- seems like they're just admitting defeat on their primary function.
"jQuery was conceived specifically to address the differences in browsers, so we’re not going to abandon the essence of our philosophy and simply disregard the millions [still using] oldIE. Yet we also want to move ahead and take advantage of modern browsers, especially the growing mobile market."
The whole point of jQuery is that it's supposed to allow you to move ahead without losing backwards compatibility. Making this split -- especially with a version number, which implies a feature-freeze for 1.9 and new stuff only in 2.0 -- seems like they're just admitting defeat on their primary function.