No. Amir would school Conor in a fight, but with smaller gloves o even in boxing gloves, like it or not, McGregor is a top striker that understands the importance of timing over speed and precision over power, something that Amir never understood.
Amir can't stand up to most flush shots. Conor has power no doubt. But if they were to fight Amir would school Conor with his boxing and not allow Conor to land flush on him. Conor would have to use that killer reverse round house to Amir's body to get him confused on how to protect against kicks... then conor might be able to faint a kick, get Khan to react to it, then get his shot in. But if it's pure boxing, Amir will school conor.
A flush shot is a flush shot. Khan's chin doesn't automatically become granite instead of cotton candy because the gloves got smaller. Not a chance he eats Connor's best shot and remains vertical. That said, if you want to change the question to: would Connor be able to outbox Khan and land a flush shot, my answer is hells no, in a boxing match Khan looks like Godzilla and wipes him out.