Notwithstanding the current level of threat in Turkey, which if I were transiting wouldn't bother me one bit, I would still avoid Turkish Airlines and pay more if necessary to go on one of your alternatives.
Turkish have had a poor safety record over the past few years, I'm afraid they are amongst many on my personal no fly list.
Use any of the ME3, or if someone like KLM or Lufthansa operate there then try one of those, beware though that LH have an ongoing issue with crew and have been plagued by strike action over the last couple of years.
This is all personal opinion, but you asked for thoughts, those are mine.