sorry for being late to the party :) but I just recently run into kind of a similar problem. Had a board layout with an atmega328p replaced by atmega328pb and using a murata 16MHz ceramic resonator with integrated 15pF caps. In my application the voltage ramps up veeery slowly (500mV / s). The old atmega328p boards dealt with it fine (BODLEVEL at 2V7), ...
No, it's not possible.
The stlink "speaks" SWD, whereas the atmega uses a completely different, incompatible, debug- and programming-interface.
By the way, the stlink v2 itself contains a microcontroller multiple times more powerful than an atmega644.