To the questions I posed here.

Here’s the explanation I received in an e-mail from Princeton University spokeswoman Cass Cliatt:

The University respects copyright and has a permissions process for reproducing items in its archives, and the material removed from the Weekly Standard’s website was copyrighted material for which the Standard did not request permission for republication.
As stated in the University’s permissions procedure for the Department of Rare Books and Special Collections (linked below), for most items in our archival holdings, Princeton owns only the physical item, not the property or copyright, and any items reproduced cannot be published without following the appropriate permissions process.
Here is the explanation for requesting permission, which the Standard did not:
http://www.princeton.edu/~rbsc/research/rights.html

This confused me, because the Standard said “links to the original articles,” not the articles themselves, had been removed. I followed up and Cliatt responded:

My understanding is that the Standard republished photos of original articles (not links to our website). The images in question are of an independent student publication (the Daily Princetonian is not a Princeton University publication). The photos were obtained at Mudd Library for personal study use only; additional permission would have been needed to publish images. Here is the policy regarding taking photos of archival images for personal use (the policy states that the images cannot be published)
http://www.princeton.edu/~mudd/research/RareBooksDigitalCamera-policy-2008.pdf

I’m still waiting to hear back from the Princetonian’s editor, who might be able to handle permission (or might want to re-publish the articles himself on the paper’s site).

UPDATE: I’m told the Princetonian will soon be re-publishing its Sotomayor-relevant archive articles.