He literally had no other options. In canon it’s either let the coup happen and eventually have his entire family being killed including him or kill his family and give his brother a chance
He had many other options he could join Uchiha clan in coup .
He could take Sasuke and run away, we dont know how things would play out if coup would happen , maybe his parents would survive maybe not.
He could just stay neutral , leave and run away , I doubt Hiruzen would order slaughter of Uchiha children .
Every option is better than murdering your own parents .
He didnt prevent Konoha civil war or anything because in reality he completely slaughtered entire fighting side in potential civil war that could happen.