I just got back from trekking to Chaqmaqtin, working on a full writeup in the next few days.
Altitude sickness isn't likely to be a problem if you stick to a normal itinerary (go Khorog, Ishkeshim, Sarhad, and then trek). The first day of the trek is the high point at 4200 meters, but you descend and sleep at 3400 which isn't too high.
But really, altitude sickness is different for everyone, and other people's experiences won't really say anything for your own.
Best thing you can do is follow the typical route, which helps acclimatize properly, and drink lots of water. If you've never been at altitude before and aren't sure about how your body will respond, carry some diamox as a precaution.
4200 meters isn't that high in the world of Greater-Himalayan trekking, tens of thousands of people trek to above 5000 meters in Nepal each year. You'll feel tired and get out of breath more easily, but that is probably about it.
EDIT: For those who come across this thread, here is my Wakhan Corridor guide