It must be agreed that the NYT certainly is not openly complaining about her being jailed. I conclude, therefore, that it does not bother them too much. Are you sayiing that is pleasing to the NYT? Their complaints are far too faint. They are simply buying time and hoping it will fade. Ms. Miller, on the otherhand, has her life turned upsidedown...and the question remains...WHY?
All pure speculation on my part ...
The NYT doesn't want to complain, because that would expose them as being subjected to Miller's control. They are the reporter's outlet, but without reporters, they have no product. It seems she hasn't been doing much work on her assigned beat anyway, and it is possible that her involvement in the Plame case (if any) is OUTSIDE of her role as a reporter. That is, while she is a reporter, any contact she had with the Wilson yellowcake story ws NOT as she was preparing a story on that subject.
I do agree, there is no harm in buying time, and if Miller is indeed the skunk, the NYT would probably prefer that fact to not become public knowledge.
Miller's motives are similer, to not be outed as a skunk-liar, to not expose the fact that news is manufactured in order to harm the administration, and as long as she is in jail, she gets cred with her left-wing friends.