According to the latest podcast from Kojima Productions, players will have to start anew in Metal Gear Solid 4 in order to gather trophies.
So, there's no way to retroactively apply trophies to existing saves, so players will have to replay the game to its full extent. The trophies were implemented as a celebration of MGS4's fourth birthday, so the timing, according to the podcast, was "perfect."
Along with this news, Kojima Productions also announced that installation will have more options. Instead of having to install between each act, players will be able to apply the entire installation at once. The old installation system was meant to counter the default small hard drives that were once in the old PS3s.
The complete details on the trophy list will be announced at the Metal Gear 25th Anniversary on August 30. We'll keep you posted as we find out more.