Having a keen sense for problems that exist, and wanting to demolish them and fix the place from which they spring is not an instinct to quash.

That it causes you emotional distress IS a problem, insofar as you have the ability to perceive and want to fix the problems in absence of the distress. You can test that by finding something you viscerally do not care for and seeing how well your problem-finder works on it; if it's working fine, the emotional reaction is not helpful, and fixing it will make you feel better, and it won't come at the cost of smashing your instincts to fix the world.