Should I choose IIT Bhubaneswar civil over NIT Trichy ECE?

ECE is in any way superior to Civil Engineering. NIT Trichy is also a really good institute, so don't just go for the IIT tag. Taking Civil in a new IIT (or even in an older IIT) will limit your options, in terms of location or something else. 

You might not get as many opportunities as you might get for ECE, given that the packages offered for ECE branches are comparatively always better. 

If you had the option of choosing a circuital branch in IIT BBS, then it would be highly recommended to you, but since you are considering Civil, it is a better choice.