We did it at Christmas with a 4 yr old and 8 mth old. I've done it twice previous to this when DD was 8 mths and on my own with her at 2 and a half. Definitely fly straight thru. We had enough time to walk from one terminal to the next on the way out (at Dubai) and to be honest it was great as there was no hanging around. Flights were horrid (but that's another story of flying with 2!) Like u say it'll be worth it for your little one to spend time with his family. You'll be fine.