imho IST is currently one of the most secure airports worldwide, right up there with BRU. It really depends on if you want to avoid it because of concerns about safety ... or because of the nightmare of additional security.

On the question of going into town, just be aware it'll be a much longer process to get back in.

On the TK vs LH; as has been mentioned it depends on the seating for LH quality. Most LH flights have the upgraded cabins but you should be able to check your flight number listing on seatguru. Of course there's always a chance of a downgrade and there are still some potential footsie issues due to shared footrest with a small barrier.

Another thought, hard to say without knowing your timings but review the connecting times. I prefer to get the shortest hop followed by the longest hop when returning home. With a short but MCT valid connection time. And if the transit time is short how many more flights are there - I'd ventue LH has lots of flights that'd get you to YUL or failing that YOW/YYZ with a short hop onto YUL.