JMM's the best counterpuncher in the businesss (outside of Mayweather). He'd have more than a chance. Khan is predictable, comes in and out in straight lines, doesn't vary his attacks, fights at one pace, etc. He'll get away with that stuff -- due to his workrate and speed -- against good/decent counterpunchers. But elite ones like Mayweather and JMM? Nah. He'd begin being countered from the opening bell. And if JMM can find him that easily, he won't need to hit as hard as Garcia to get the stoppage. Never underestimate the danger of pin-point accuracy and timing.
This really says it all. Khan's technical ability is almost completely biased towards his speed, with no real lateral movement or inventiveness in putting his punches together. The same speed that fazes lower level fighters would have little to no effect on JMM, who would counter and pick him off at will. JMM by late stoppage, imo.