That will depend entirely on what direction he wants this team to take. If he wants a complete blow it up and rebuild direction, then he really wouldn't care where he trades these players because they won't be key guys for their new teams once we are good enough to contend.
However, if he is interested in rebuilding on the fly, then I agree that he would prefer to trade then to Eastern Conference. But again, it would depend on what he would get in return for them. If he were to hypothetically trade Artest to Cavs and they were offering Gooden, and Suns were offering Marion, of course he would trade him to Suns.
Its not unreasonable to think that Petrie would be willing to trade players for the best possible deal, regardless in which conference the player would play once traded.