There's a world of difference between a dude that flees the jurisdiction and a dude who's thrown out of the jurisdiction. The former may well not be able to appeal his conviction, but the latter can. It's one thing for a court to say that a guy has to take the bad (his conviction) with the good (his escape from justice). It's wholly another to say that someone had to take the bad (his conviction) with the bad (his deportation).
Regular litigants often make a number of extraordinarily bad arguments, on the theory that it's sometimes worthwhile to throw a ton of stuff at the wall and see what sticks. But that principle usually doesn't apply to attorney general's offices, who are able to take a broader -- and more informed -- view.
But there's an exception to every rule. This one's one of 'em.