Had Rove and President Bush simply stayed out of this race, they were more likely to get both 4 more years for Bush, and a non-RINO Pubbie from Pennsylvania (with Kyl likely running the Judiciary). Now, if they're lucky, they'll either lose the Electoral Votes and keep Scottish Law (most likely), or get the Votes and lose the seat.
To amplify on that, let's consider what a Toomey win would have done in November versus what Specter's win will do. Toomey would have created the same "clear difference in opinion" in the Senate race that exists in the Presidential race, with virtually no cross-over. True, it would tighten things up, but with a "slate" type of election, the race at the top is most important. That race is in Bush's favor.
Now, however, we have Specter. Which of the two scenarios (or the darker lose/lose scenario of Kerry and Hoeffel carrying Pennsylvania) happens depends on 2 things; where Specter's late support in the primary came from and whether the Toomey supporters ultimately bite the bullet one more time. A Specter-Hoeffel race doesn't have a "clear difference" since Specter is a liberal. Not only will a bunch of primary Specter voters (those that obeyed the RAT Masters and reregistered as RINOs) revert back to the RAT Party fully in November, but a small chunk of voters (enough to make a difference) will go with a Ke(rr)y/Specter ballot.
Meanwhile, despite all the consternation around here about boycotting the Senate election (and to a lesser extent, the Presidential one), most of the Toomey supporters will ultimately decide that the risk of a "majority of VP" in the Senate is not worth "sending a message". To the extent that they stay home or otherwise send a "protest" vote, however, the chances of a lose/lose are greater.