You want to be able to lift the glass panel out of the insert to clean it. Otherwise you will end up with dust and crumbs around the edges making it hard to clean and it will look like hell. Do not glue it in!
**Sicks Ate **is right. I would cut the desired size hole in the desk, router out an edge of the hole to a depth, probably about 3/8 inches for a this panel of glass, for the glass to lay into, leaving a ledge that the glass will sit in, and just drop the glass in. You can then just push the glass out from below, clean the area, and put the glass back in. This is how my last glass/wood coffee table was built. This assumes you are putting the glass panel into a level desk.
I would go to a glass shop and order a piece of tempered glass to fit the hole you have created. Tempered glass is much stronger than regular glass and if it breaks it will turn into little corn sized chunks that wont send anyone to the hospital. Most glass you see used in desks or tables is temp glass.
With tempered glass you have it order it to the exact size that you want, it cannot be cut after it is tempered or it will also turn into little corn sized nuggets.
So build your desk panel first, measure for the glass, order glass, drop in. That is the way I would do it.