Yes you MUST remove it all, leaving it would be a big mistake on a number of levels.
First off, there is GOING TO BE rust in that channel. I have done way too many of those GM window channels to count and I have NEVER, make that NEV-ER seen one that didn't have some rust that needed to be cleaned up and primed, and only a few with only rust, they most always have rusted holes. The clip studs are often broken, there is just no reason what so ever to leave that junk there.
Now the next decision, do you use the Butyl tape or do you have a glass shop set it in urethane? I have done a pile of those windows on butyl and it seems to work fine if you have covered all your bases. Some worry about the structual aspect, but realistically in my opinion this isn't an issue for a number of reasons. But your car did NOT come with butyl as I thought for years it did. It wasn't urethane either, I think kinda in the middle between the two as far as strength. But non the less, having a glass shop install your new windshield on urethane could be a good way to go. You can do it your self but the learning curve is pretty steep and I would say have someone do it.
Here is a "Basics of Basics" on setting glass. I added a disclaimer at the end warning about using butyl tape because I was getting such flac. But really especially on the back glass I don't see a big deal. But it is a choice for you to make.
"Basics of Basics" Window Setting - Team Camaro Tech
And you are going to want to sand blast your channels and apply epoxy primer by the way.