I believe they both work/or worked in Philly legal circles for years. Specter might not like his abortion stance, but it'll be difficult to stall a local. These Senators take pride in their "own" SC nominees. At any rate, their relationship is worth exploring. I suspect it is part of W's strategery.
If anything, Specter might interpret this nomination as a thumb in his eye. Specter's been very clear about where he stands on abortion and judges, and there's not much mystery about Alito. Had he been asked, I think Specter probably would have blackballed him.