What happens when you go to Options screen, set the detail level and resolution there and then restart the game? Does the warning appear again? Does it appear and also reset the settings to lowest setting, or does it just appear and warn you that your sys. might not be good enough?
If its just the warning, it might be annoying but i think a typical civ game lasts a few hours anyway so no big deal.
Also, i cant verify this with my current system because its quite high end so for me this warning does not show up. But iirc 2 years ago i had a slower system with a radeon 4670, and with that this warning would pop up on the first start of the game. But i think after i went to options and set them manually to medium settings it disappeared, not sure though..
Also, you might try to change 0 to 1 for this setting in CivilizationIV.ini:
; Don't show minimum specification warnings
HideMinSpecWarning = 0
The config file is in the folder
My Documents/My Games/Beyond\ the\ Sword/