If this happened to me, I'd be equally upset and mad as hell at TK. You were a little short for time, but they could have been a little more customer friendly! I think I would put in a claim with my credit card - you can't lose one way or the other. I have heard similar stories of problems with TK ground staff, and this is the reason I avoided them. Generally, I found most Turks to be extremely cooperative - much more so than Americans are! Seems to me this should not be blamed on Expedia!
This surprises me at Istanbul, because I had a very easy passage through IST, myself, in October. I flew Air France to/from CDG and had no problems, but I do always arrive with plenty of spare time. My return flight was at 9:30am and I took the 6:30am Havas shuttle from Taksim - probably arrived at IST close to 7am. I stopped for 20 min to get my pack shrink wrapped and then walked over to AF checkin and went through extremely fast, no lines at all, pack checked through to JFK by a really friendly Turkish lady. Flight was packed, but AF got us to CDG on time and a pretty good flight.