Yes, I should think so, It can't stay on the pad for 6 months, and also 39A will be needed for other launches.
The payloads will probably be have to be unloaded from Atlantis and go back to the PHSF, a climate-controlled environment. New payload carriers will also have to be designed.
Atlantis will now not be available for other missions.
A new back-up shuttle will have to be made available for STS-125, so that wont be available either, so some missions may have to be cancelled
The crew will have to do more training.
STS-126 preparations will need to be speeded up.
Pad 39-B will not be able to be handed over to Project Constellation, as it will be needed for the backup shuttle when STS-125 does finally launch (probably in Feb 2009). So the Ares I tests scheduled for Feb will have to be cancelled.
Other shuttle missions will have to be re-organised.
It will really set back NASA's entire program.
--But on the plus side, at least there will be more time to work on the STS-125 payloads addon--
