Maybe it doesn't matter much, but I assumed that Alton wasn't Jaime first cousin, but maybe second or third. He didn't know who Alton's mother was, and I would have thought he would have kept track of his own aunts. But if she was Tywin's cousin or second cousin, that would be another matter. Plus, I don't think Alton would separate that much between his family and THE Lannister family if their parents were siblings.
It's still kinslaying, but perhaps a "milder" form than most people assume.
EDIT:
Also, people overlook a fact that was revealed in AFFC.
When Nymeria had mauled Joffrey and Arya had run away, Cersei wanted Jaime to find her and kill her, and Jaime stated that he would've done so without a second thought, if only he had found her first. Killing Arya would have served no purpose whatsoever, as neither Jaime or his family was in jeopardy if she survived. So tell me how killing Arya is in-character for two-handed Jaime, but killing Alton isn't.
Edited by The Monkey, 15 May 2012 - 10:08 AM.