Part of running a successful public campaign is understanding where the pressure points are and how to use them. Part of the reason to use your pulpit to make political endorsements is the implicit threat that those endorsements can be withheld or withdrawn. It's a level of power to be applied where possible.
I wasn't too thrilled with NARAL's way-early endorsement of Linc Chafee over his as-yet-to-be-determined-but-pro-choice Democratic opponent but I didn't think it was the biggest deal in the world. It's premised in the false belief that maybe, just maybe, some moderate Republicans will come along and save us. They never do. They haven't bothered to do that in some time.
There's no reason fo NARAL to support any Senator who voted for cloture especially when their opposition is going to be a pro-choice Democrat who could help flip Senate control to the overwhelmingly pro-choice party. They entire purpose of standing behind moderate Republicans is the hope that they come through on hard votes. Chafee's yes-on-cloture-no-on-Alito vote did nothing but provide him with slim cover on his left flank for his upcoming re-election. He doesn't deserve the support of any organization dedicated to women's reproductive rights.