This is like saying Chemistry should be merged back in with Physics as one is just a deep study of the application of the other. The edges between related departments are always going to be blurred, but it's still practical to have things separated out into different departments. I think that we'll just continue to so lots of faculty with joint or honorary positions across several departments. Hopefully this will also encourage students to collaborate in a more interdisciplinary way, too.
I don't see anything merging back. The trend towards more and more specialization and compartmentalization has been going on forever and there's no reason to believe it will be inverted any time soon.
My alma mater (The Ohio State University) has multiple Computer Science programs. There is an Associate program, an Arts & Sciences CS program, and a computer Science & Engineering program which is part of the Engineering school. I could see the Arts & Science program merging with the Math department, but the Engineering school will most likely hold onto the CS&E major.