How can I modify the Civilization IV keyboard commands on OS X?

I think keyremap4macbook might help you. It can enable a number pad. It's how i played civIV. I believe, you just need to press the fn pressing the "numpad" keys.

I don't have Civilization so I can't confirm this but holding the fn key (bottom left of the keyboard on a MacBook Pro) causes the keys around the right hand home-row to work like a number pad. These keys have the numpad key they correspond to in the bottom right corner of the key. For example fn+M=num0, fn+L=num3, fn+U=num4

I'm not familiar with keyboard shortcuts in Civ IV so there may be some negative overlap (7, 8 & 9 are the same key for the numpad and top row numbers) and pressing the fn key can be a little awkward but this should at least let you use numpad controls.