He also threatened to veto the NDAA[1]. I wouldn't put my money on him vetoing CISPA.
[1 http://www.ibtimes.com/why-did-obama-sign-2013-ndaa-after-th...]
[1 http://www.ibtimes.com/why-did-obama-sign-2013-ndaa-after-th...]
So yeah, he actually likes the bill and the likelihood is that he will sign it or some form of it. The veto threat is just part of the dance.
Also, the brouhaha over that bill is over how it might be interpreted in a parallel universe where Hamdi v. Rumsfeld doesn't exist.
As the President cannot veto part of a bill, vetoing the NDAA over those provisions would literally mean vetoing the entire defense budget.
They obviously don't have to listen.