Board Thread:False Info and Speculative Discussion/@comment-124.148.190.247-20140708153114/@comment-19765459-20140710030633

Emotionally devastated as he doubtless was when Allison was killed, Chris probably felt the need to have someone to cling to, just for the sake of not breaking down into total wreckage. While the reasons he seemed to be treating Isaac as a trainee hunter remain a mystery (as with so much else that happens on this show), there were always little hints that he cared about Isaac despite the latter being a werewolf. At least they could commiserate over Allison.

It's a reasonable (if buried in subtext) explanation for Isaac's absence. You could even use it to explain why Chris doesn't bring Isaac back with him if he does return to Beacon Hills because of Kate. He wouldn't want the last person he cares about killed by his psychotic, back-from-the-dead, were-something sister. Isaac is naive enough that Chris could go back to the U.S. on a "business trip" without him automatically following.