1) On One Hand: Super Glue is Flammable
Super glue--the common name for cyanoacrylate adhesives--is highly combustible. When heated, super glue becomes unstable and gives off hazardous fumes, according to the Occupational Safety and Health Administration, which produces a Material Data Safety Sheet on these kinds of adhesives.

2) On the Other: There are Microwave Safe Adhesives
Several adhesive manufacturers produce non-toxic, microwave-safe glues. These adhesives are appropriate for repairing most cookware material, including ceramics, glass and plastics. Microwave-safe glue may be used to make cosmetic repairs to external, non-mechanical components of the microwave and as a temporary fix to the appliance's rotating glass tray before it is replaced.

3) Bottom Line
Neither super glue or microwave-safe glues should be used for interior repairs to a microwave. The Material Safety Data Sheet for cyanoacrylate adhesives specifically warns against exposing super glues to heat. Microwave-safe adhesives should also not be sued to repair microwaves with large holes in the door or in the interior; appliances with these kinds of holes can leak microwave radiation and should ultimately be disposed of.