I would imagine the ABC affiliates have a lot of mixed feelings about this. ABC's long-term goal of getting Kimmel set up to be the established 11:35/10:35 show when Letterman and Leno retire, in many cases, will not match up with the affiliates' short-term profit goals. Some ABC affiliates like having "Nightline" right after their local news because they feel it compliments their news. Add to that, "Nightline" has done pretty well in the ratings in recent years. On the other hand, there are still a handful of stations that delay "Nightline" (and Kimmel) by 30 or 60 minutes so they can plug in syndicated shows and sell most of the commercial time locally. It doesn't necessarily matter if those stations win the time slot locally, but they make a nice profit from all the local revenue.
That said, I think ABC will have to do some serious arm-twisting to get those stations not already clearing the network in pattern at 11:35/10:35 to do so. For one thing, the switch will happen in January. Most stations will be in the middle of their syndication deals and it would be tough for them to shift shows around even if they wanted to. A switch in the fall (say in a year) when syndication deals are up would potentially get ABC a little more leverage. However, if Kimmel really flies at 11:35/10:35 in January, some of those stations not airing the network in pattern might be more inclined to do so come next fall. In reality, I'm pretty sure Kimmel will rank third behind Leno and Letterman, and those affiliates delaying ABC late-night programming will continue to do so.
As far as "Nightline" goes, I think the switch to 12:35/11:35 will be the beginning of the end of the show. The older folks who currently watch "Nightline after their local news won't stay up an extra hour (let alone sit through Kimmel) to watch it. In most cases, I doubt the content of most "Nightline" shows would be compelling enough to see a lot of DVR action. I would imagine the higher ups at ABC are already knocking around in the back of their heads what kind of show they will put on after Kimmel when "Nightline" bites the dust. I guess if Kimmel and "Nightline" both do really poorly in their new time periods, ABC could pull an NBC and put the shows back in their old slots.