Why did 47 leave his crucifix at the end? The obvious answer is because he chooses to be an assassin over believing in God but it's obvious in later games he continues to believe. Then you realize he returned to being a hitman voluntarily after losing Father Vittorio. 47 may believe he's unworthy of redemption after that.
"Tobias Rieper", aside from pun on "to buy a reaper" and an obvious red flag, also ties in to 47's hidden heart. Tobias is a translation of "Toviyah", which means "God is good", fitting for a devout Catholic. His name translates to "good killer".
From the 2007 film - the viewer may wonder why 47 had a key to the cathedral in his hotel room, if he didn't plan to use it until after his room was raided. Mike speculating that 47 intended him to find and use it doesn't hold much water, since 47 doesn't arrange that part of the plan until much later and the FSB nearly seize it anyway. However, then you remember 47 being annoyed because he'd planned a more subtle approach to kill Bellicof, meaning the key was an artifact of his original plan that he ended up not using.
From the 2007 film - the person in Mike's home 47 has killed may not be some random person. It could be a fellow agent which was sent to kill Mike because his investigations into 47 would have placed him very close to the Bellicof conspiracy. 47 could have in fact, saved Mike and his family's life, something he started doing halfway through the film at Nika's insistence.
