Kojima isn't the only guy responsible for making all of these games yes but that's not the point.
If you have a name that you think can step up to the plate to take responsibility to Silent Hills I would like to hear it. It's not just about making a Silent Hill game, cause any developer can do that, but giving it a shot at greatness again.
I'm not the right person to answer this, because I think the MGS games are horrible, so I'm definitely not the one to name likely very talented people on the team, but honestly, I wouldn't have named Aonuma after Ocarina of Time either, since the marketing and press focus was on Miyamoto, so I dodn't know anything about Aonuma before MM. But let me give you another example based on what really happened: Yuji Naka left Sonic Team after Sonic 2006 - Naka, the guy who was marketed as
the guy behind Sonic, the team leader for many many years, with main responsibility for excellent games like Sonic 2 and NiGHTS. Takashi Iizuka takes over and reboots Sonic with the best 3D concept they've yet had, Sonic Unleashed (the boost direction that was the basis for the great Colours and Generations game was taken in Unleashed).
I do not know who can be the Aonuma or Iizuka of Konami, but writing off the whole studio because of one man's departure is dealing the whole team so much disrespect that I, as someone who does not like their work, feel bad for them. But anyway, good candidates to take over Kojima's responsibilities would be people in positions such as director, lead game designer, lead level designer, concept & planning, this would be positions where usually very highly regarded people within the team do their work.