I think you only need to disable Crossfire when you have multiple cards, not GPUs. I have two 5970s and I had to remove the Crossfire cable that connected the cards, but there's nothing you need to do about the two chips on your card.
If you're only talking about a single 5970 card (which contains 2 GPUs), then you don't have to disable anything, as far as I know.
It's only problematic when you have two cards. Then you physically have to remove the Crossfire cable. I'm not aware of a software solution in this case...
I have 2xHD5970; to disable crossfire in windows, when CCC detects a second card, it enables a crossfire menu; in it you have a checkbox to enable/disable crossfire. In linux you have an aticonfig command to do that.
Note that in windows, if I disable crossfire, I only find 3 GPUs in clinfo, to see 4 GPUs I have to enable crossfire (My development cycle starts in windows and the pass to linux, so I didn't checked it in linux yet)
hope this helps,