Yes, I think she cares that he's leaving - in the sense that he wasn't poached from another network. Her
own network took a look at her show, didn't think their partnership was so spectacular that they wouldn't dream of breaking that partnership up or changing a thing, but and decided to dismantle it, to take Michael and put him on a different show they own, where they thought he'd shine and do good things for that show instead.
What does that say about Michael and what he thinks of Live? He willingly is leaving a show where he is one of
two stars, getting equal airtime, to go be on a show where he will be one of
six stars now, and not one of the two head stars.
As for Kelly, her show is uncertain now. The show's success depends on if they can find a good partner for Kelly. It took them months the last time. Kelly can't carry the show on her own. All the great men who did really well and that most people thought she paired up well with, all have successful careers of their own already. They don't NEED Live. And perhaps that's why they did so well with Kelly. They are confident, strong personalities and already a success in their genres. Anderson Cooper has his own show on CNN and is also on 60 Minutes now. Neil Patrick Harris got a Tony Award last year for being on Broadway. Josh Groben is a fantastic singer.
That early morning venue is hard to fill. While the rest of us minions are used to getting up and going to work 5 days a week at 9am, TV stars find that unappealing, a grind.

So they have to find someone, not very successful already or so well known he out-shines Kelly. And it has to be someone who has has chemistry on TV with her and is willing to let her be the top dog. And it probably is going to have to be someone who can stand her off-stage too, and is willing to stay a lot longer than Michael did.
If they can't find someone compatible, her show's ratings will go down. It may also go down while they are trying to find someone. That might get the show canceled. That all affects her. Instead of being able to go on summer hiatus and relax, she may be worried about the future of the show. So, yeah, she cares.