This will have no effect on consumers for a good while. Keep in mind that this has months, even years, of regulatory morass before the companies are truly merged and until then certain amounts of separation must be maintained.
Even after that is done, you're unlikely to see ATI support for Intel systems dry up. On the board level, things will continue to be based on the PCI-E open standard. With the 5 Gb/s version still in the draft stages, there isn't going to be a shift away from PCI-E as the standard for a very long time. At least a decade.
On the chipset level there isn't much to lose. You may have seen reports that Intel was 80% of ATI chipset income but they usually fail to note that PC chipsets are still a new business for ATI and a very small part of their revenue picture. Losing the Intel motherboard market doesn't change much going forward, especially when they'll be gaining a favored position in AMD branded motherboards. (In the same way, Nvidia loses some of their AMD business but picks up more Intel business.)
AMD has long been disinclined to produce their own chipsets for their own CPUs and even less their own motherboards. But those factors are critical requirements for taking away some of Intel corporate desktop market. Vendors and big corporate buyers both like that they can get a single complete board from Intel, drop in an Intel CPU, add some RAM and that's all the silicon for a PC. (Hard drives have their own silicon but since they're self-contained it isn't viewed that way.)
AMD could have picked up all the elements ATI offers to PC integration for a lot less cash than buying ATI but the strong ATI consumer product market is what makes the difference. It will do a lot to boost AMD's revenue picture despite the debt load incurred from the purchase. Both AMD and ATI have lesser margins than their competition but they're generally profitable.
The primary goal here is to create a single entity with a superior combined revenue than the two of them separately. That means little change to either company's business for a good while.