I never thought about that... that's interesting... So, pure speculation (obviously), but there are a few possibilities.
(1) The Architect is an uninhibited computer program, like the Agents, and would therefore have similar or greater powers.
(2) The Architect could have some sort of "supernatural" abilities like teleportation or telekinesis. He might even shoot lightning like Palpatine.
(3) The Architect serves a specific function - this grandfather/tyrant - and does not have defensive capabilities. He wasn't able to predict Neo's response, so he probably assumed that, like the antecedent Ones, Neo would not attack. He didn't, but could have, but maybe the Architect just wouldn't assume that was necessary.
(4) My best guess is that the Architect would just disappear. He'd "jack out" of the Matrix and head somewhere else. He wouldn't fight or stop Neo from fighting, he'd just go away. He'd run.
The results are worth thinking about, too. If Neo could kill the Architect, what would happen? I assume that he was just a program and could be replaced or has a redundancy somewhere. Neo couldn't really stop him (which is maybe reason enough to assume Neo wouldn't attack). My guess is that killing the Architect would do very little. The machines could always just code up a new program. It might cause some system malfunctions for a brief period of time, but that's about it.
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