The onboard should be able to play Civilization okay
Sure, if you're talking Civ 1 or Civ 2 but not if your talking about Civ 3 or definitely not Civ 4.
That is a 5 year old machine. I would recommend replacing the whole thing for about $500 and he'd see a huge performance increase, even in a 2 year old game like Civ 4 (unless he only plays on small maps at low resolutions).
If he only wants a replacement video card then I would see about getting an AGP card off of ebay for $20-$30 or if he wants new one then get it from a place online like Newegg. However, he'll be paying a for a card on a dead socket. We've moved off AGP for a while and they don't make modern graphics cards with AGP.
I looked through Newegg and was surprised at how expensive these cards are since they are all old cards. The best I was able to find at a reasonable price was the SAPPHIRE 100298L Radeon HD 3450 512MB 64-bit DDR2 AGP 8X HDCP Ready Video Card - Retail for $49.99 :
http://www.newegg.com/Product/Produc...82E16814102862
If you decide to go with something else then I certainly understand but stay away from those GeForce FX 5200 or other 5000 series cards. I noticed a disturbing number of these still available. Those are absolutely terrible cards and I wouldn't recommend them to my worst enemy (I had one of these cards when they came out).