I use a X1950pro & also a 690G.. AA & AF works fine on both GPUs in Sacrifice if you force them on in the CCC.
If I remember correctly, my old 8500LE works with 2x AA in Sacrifice too. :)
I never bothered with the anti-aliasing option in Sacrifice as I always force it on in the ATI CCC.
The 690G struggles with anything more than 2x AA & 8x AF though, whereas I could use 6x AA & 16x AF on the 1950pro.
I do have some problems too:
1) Disappearing 3d models with the widescreen hack(left it off in the end)
2) Occasional tearing textures when the camera is rotating or at a certain angle. (Had to use non T&L mode to get rid of them)
Perhaps the visual issues with AA are only present in newer ATI cards(2xxx & above).

Btw dainbramage, from your screenshots, it seems that Dot3 bumpmapping is not enabled.
Dot3 bumpmapping is an option in the game Graphical Settings if Sacrifice patch 3 is installed(I think the GOG version is already at patch 3).
Try it with Dot3 bumpmapping & see if it helps.

I have normal mapping enabled rather than bump mapping...
It also shouldn't make a difference to the 2D panels or the sky either way.
EDIT: Using bump mapping = ugly effects still there.

I'd guess it's the sacrifice engine only being optimised for an nvidia card rather than a bug with ATI.

*Bump*
Has anyone else with an ATI card checked what I saw? I'm getting similar issues with fallout 3 (to a lesser extent, though), and as my card is supported, I can hardly blame compatibility issues with the program (or the program being old). I'm in the process of re-downloading my driver, will update later.
EDIT 1: Man, Toshiba REALLY needs to update their bloody drivers.
EDIT 2: Re-installed driver from Toshiba - no change. However, their drivers are ancient. I'll download directly from amd and try again. May have to fiddle with the mod tool.
EDIT 3: Okay, properly installed everything new now, Sacrifice is still screwy. FO3 better work...
EDIT 4: I'd still like someone else to confirm, though. Shouldn't take long, just turn on 2x AA through the toolbar, open sacrifice, go to elysium/ethereal realm and look at the sky, post whether it looks normal or not.

I run a Nvidia 6800 and it is selectable. I put everything to high in game with AA on and it all runs smooth.

The artifacts with AA does not occur on the X1250(integrated X700) or x1950pro.
I guess the issue could be for ATI Dx 10 cards or just the HD2xxx series in particular.