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.