I tend to almost want to go with this explanation. If you watched the Animatrix one of the shorts depicts a group of humans disabling and then capturing several of the machines. The group then jacks into the mind of the machines and helps them become sympathetic to the humans cause. Of course new machines come in and kill everyone at the end of the short, but who is to say that the a few machines couldn't have been "convinced" in this manner to jack in and protect certain aspects of the matrix. If we're going to travel down this route one could also argue that if Seraph is a machine himself that he may have been put there as a safeguard by the machine world. Seeing that sometimes certain programs go rogue (i.e. Merv and Agent Smith) it would make sense to put a device in place to protect the two programs in the matrix that strive for balance. So the Oracle has Seraph and The Architect had a nearly impossible to defeat "hardwired" entry deterrent system. It would be beneficial to the machines to ensure the safety of the programs that make sure that the world inside the matrix doesn't wipe itself out. Just my 2cp.

**It would appear that pain killers and muscle relaxants make writing out clear, concise, and gramatically correct sentences fairly difficult.**