Hi there Fam and welcome to the forums .......
What i have found the (easiest) for me to do is when using the remote on the ATV2 i put a little something over the IR Remote sensor on my MBP and happily use the ATV2.
It doesnt bother me doing the the other way as when im using the Remote for the MBP my ATV2 is on the HDMI channel that i chose to put it on and i can never see it being on. I have it on sleep after a Hr so im not worried about the power it uses.
Or the other solution is (if you have a iPhone or iPod Touch) is to get the
Apple Remote.app from the iTunes Store and use this for the ATV2, which wont effect the MBP.
SO there are a cpl of solutions but if you dont want to see that tiny light on the ATV2 when you use the Remote with the MBP, best bet is to put something in the way of the Sensor or to hide it ......
Cheers