Trying to understand negative voltages
It is totally possible to power the MCU off a -5V rail as you describe. 

The person who told you about spikes in the "GND" which becomes the MCU VCC pin should be aware that spikes could just as well show up on the -5V rail. The MCU can be over voltaged simply by applying too big of voltage difference between the MCU VCC and GND. 

The main downside of using the -5V supply is the implication that it comes into a system that also has a +voltage rail or two. Any circuitry in the system that uses such +V and the "GND" as its supply will not be able to interface directly with the MCU. Special level shifting circuitry would have to be applied to translate the negative domain voltages of the MCU to the positive voltage domain of the other circuitry. 

If the system power supply is just the single voltage rail that you describe as -5V then just switch the leads around and consider it a +5V supply.