Is my ECU/electronics gonna be fried??

I was trying to diagnose a bad alternator earlier today on my mustang. I did the old method of starting the car and unhooking the positive terminal. Supposedly if the alternator is dead and its running off the battery, it will die. Well my car kept running which means the alternator is good but after about 30seconds it started smoking so I shut it off. I have run across a couple articles online that say you should not unhook the battery on a newer car cause it can cause voltage spikes, I hope thats not what caused the smoke. Do you guys think I will be ok, do you think a wire or the computer might be fried?

Honestly, it was running a little bit rough after I did that. It has not thrown any codes which is odd. It originally died on the interstate while driving at a constant speed. The battery was pretty much drained so I figured the alternator went out but I guess not Right now it is 40miles from home in a small town mechanics parking lot. Hopefully he is decent and can find wtf is going on. I haven't caught many breaks this weekend