Whether or not you think being choked out is acceptable as a regular event in your training, the reason it happened is that you are inexperienced with gi fighting. Just like the first time someone gets put in RG, they don't know they are in trouble until it is too late. If you fight with the gi, you will learn to gauge when you are in danger. The fact is, gi chokes usually are really tight, often painful, and extremely effective - they force you to defend them, often in only one direction. In the same way, don't fight scared of chokes. It will actually make people go for them more, and it will ruin your other game. If anything, get in them and ask better fighters what you should be doing. I started no gi on my own, and got ezekiel choked like 20 times a day for a while. cross chokes, loop chokes, etc. - they all crushed me, and everyone knew it. Now it is damn hard to choke me out (relatively), and I see the openings that used to plague me when I am in the opposite position.
Here are the other reasons you should still train gi sometimes. If you are training in part to actually defend yourself in real life, you may have a collar on you when you fight, so learn to defend it (and attack with it). Also, I noticed that when I train nogi, my gi game gets better, and vice versa.
In the meantime, here's a few tips. 1) Most chokes can be stopped by simply opening up one of the guy's elbows. They can't get the angle or pressure. 2) If your opponent has a single hand with a deep grip in your lapel that you find threatening, always turn into it. In other words, one direction you turn tightens the choke, the other opens it. Always go the latter, or you are done. 3) With a gi, it's extremely important to keep your chin down and your arms t-rexed almost always.
Good luck, hope that helps!