I agree it would have been very strange for the letter to be signed by both Tim Cook and Scott Forstall. For one thing, it would make Cook look smaller than Jobs, who, if I recall correctly, never had a co-signer on such a letter. It wouldn't have looked much better for Cook if Forstall had signed the letter alone, given its significance to the company and its customers.

My guess is that Forstall refused to sign off on the public apology. Nobody was asking him to sign the letter, but he was asked by Cook to stand behind it. Failure to do so was probably the last straw for his remaining in an active role at Apple (a role he clearly was at least contemplating leaving after his big stock sale).