Can you get a medical waiver for gastric bypass for military service?

In short, yes and no. It all depends on a number of varying factors. Examples:

1. Are you otherwise physically fit?

2. How are recruiting levels in the area?

3. Will you be able to carry out your duties as an enlisted member of our armed forces?

So, yes it could be given a waiver, but only the sole commanding officer reviewing your waiver will make that final decision.