K.D.
There's no easy way to address it without just coming out and saying it. But maybe one day when she lingers, when she comes to pick him up say, "Oh, Tommy had the worst morning. I've noticed that when you are quick to say 'goodbye and I'll see you later' that he is always so much happier. I think that when you linger to say goodbye, that it worries him that you might not be coming back. And when you are quick, he realizes you'll be back soon and has a great day." Then if she thinks she should linger, say, "You know, I've read a lot of articles that state that kids honestly do better when their parents are upfront about where they are going and when they'll be back instead of making a big deal about it." And then have a couple of articles to back you up.
I think it's a hard thing for mother's to learn, but it's really in the best interest of the child. Good luck!