That encounter obviously had a profound effect on him and provided the tipping point that led to his position on the Sokovia Accords. Seems like a compelling enough reason to me.
It would be a compelling and acceptable reason if the following 4 points didnt go against Stark:
1) He has witnessed first hand what people in authority of large scale operations are capable of. Obidiah Stane who was Tonys business partner, dealt with 3rd world terrorists, supplied weapons to enemies in wars and tried to take over Stark Industries for sinister reasons under the veil of friendship. The first movie establishes Tony cant fully trust anyone associated with his weapons business (which is 1 big reason he tries to shut it down), he can only trust himself and Pepper.
2) The whole plot in IM2 is Stark adamantly refusing to give over his tech to the government and publicly snubbing the Senator (who later is revealed to be a HYDRA member) in the enquiry hearing. This is a direct result from his experience in IM1; not being able to trust his weaponry in the hands of outsiders, no matter how official or high their rank is.
3) Going to Dennis Renyolds original point, SHIELD was found out to have multiple HYDRA infiltrators within the organisation. They managed to take over SHIELD and were seconds away from wiping out millions of targets - using Helicarrier technology developed by Tony Stark himself. Winter Soldier revealed the realistic character change in Cap where he now no longer can trust his superiors in office. Although Stark isnt in the film, you can imagine his position wouldnt be too different.
4) In Age of Ultron, Wanda and Pietro reveal a Stark label bomb killed their parents when they were young, which turn them against the Avengers. So Starks weapons killing innocent civilans has been going on for decades. To believe that hed do a complete 180 on his position after some grieving mother roasts him is a big stretch. But also the incident that killed this kid was Ultron, made and developed by Tony Stark alone. To turn around and say The Avengers need to be put in check collectively, when not only was it not their fault but The Avengers also saved the world by cleaning up Tonys mess, is astonishingly arrogant and egotistical from Stark. Tony should be put in check, not the Avengers.
All combined, theres no way to believe realistically Stark would take the stance he did in CW given previous film history. No way. Its poor, sloppy contrived writing just to create a conflict when theres no organic reason for it to exist.
You can say, "thats character development, its a good thing". But its poor character development, and that certainly isnt good.