For some reason, the standalone installer insists on installing DX, even though I'm already up to date. I suspect this was the cause of a few system stability issues and I've reverted to a restore point before it. Anyway I can avoid it this time around? I just want to update Civ, not (re)install DX.

It doesn't install DX, it installs the redist updates that have been issued since direct-x 9c was finalized. Of which there have been quite a few. There is 3 or 4 Redist's a year. The new files improve support for GFX cards and features.

Even if you have installed the most recent June 2008 Redist, the game will still pause to check if you're up to date.

If you've had sstem stability issues, you may want to consider updating your GFX drivers. Which is almost always a good idea after a DirectX update.

And no I don't believe there is a way to bypass DX. As far as I can tell theres no way to unpack a InstallShield v12 cab outside of their (InstallShield's) pricey developer pkg.