I'm not sure whether the filibuster deal is a good one or not (although Lord knows it's nice seeing Frist twist in the wind). But I can think of at least two reasons why "kicking the can down the road" could be a good idea, despite Josh Marshall's take.
(1) According to the polls, the ONLY thing the Republicans had going for them in this fight was that only a small percentage of the public knew what was going on -- on NPR today, I think they said that only about 30% were aware of the filibuster fight at any level whatsoever, and of that number, even fewer likely had any significant background information. Significantly, however, of those who did know about it, a pretty strong majority was in favor of keeping it.
If the filibuster issue arises in the context of a Supreme Court nomination, rather than relatively obscure circuit court nominations, the Republicans will have a much harder time keeping it under the radar screen, and public opinion could come even more into play on the issue. Also, it would then be apparent that the ONLY purpose in changing the rule is to allow the lifetime appointment of a radical Neanderthal.
(2) The other significant point is that had the judicial filibuster been beaten back by the Republicans, there would almost certainly have been a rush to the door by at least Rehnquist and O'Connor, since Bush would then be able to appoint virtually anyone to their seats. Without that guarantee, their leaving becomes much more problematic, making it that much more difficult for Bush to pack those two seats with relative youngsters who could be expected to continue holding back the tide of modernity for another forty years. In the best possible case scenario, they are sufficiently uncomfortable with the battle over their potential replacements that they do not resign prior to the 2008 election.
Of course, as others have said, there may also be side deals that would make this deal more palatable. But even without such secret agreements, the fact is that "kicking the can down the road" may result in our being in a better neighborhood when the can has to be opened.