Update #2: RelyOnHorror has provided a response from Konami’s North American PR regarding their original rumor: Konami Claims Recent Silent Hill Rumors Are False:
“We’re aware of all the rumors and reports but can confirm that they are not true. I know it’s not the answer your fans may want to hear,” said the Konami US PR rep. It’s not to say we are completely closing the door on the franchise, just not in the way it is being reported.”
It remains to be seen in what way Silent Hill will make a return, but does seem that the detail of Sony and Kojima getting to work on it could’ve been too good to be true. Then again, it could be that PR is just not ready to announce pending deals in progress, or that they were in talks for such a deal but it might not work out in the final stages.