GLaDOS says all Aperture devices can withstand tempertures of over 4,000 Kelvin. However, when hit with an Energy Pellet, the Gun disintegrates, thus making the Pellet over 4,000 degrees. This means that the Companion Cube and Turrets are Stronger then the Portal Gun and to whit does that mean the incinerators may not have actually destroyed our favourite friend?
It could all be a psychological test by GLaDOS (or she was fucking with us again) and CC is fine. Though with that logic didn't we drop GLaDOS in a similar incinerator..