So was Egypt better under the Muslim Brotherhood than the military junta? The "means" of their overthrow were certainly bad (a military coup), so does that automatically mean it would have been better for Egypt to have continued to be ruled by the Muslim Brotherhood. Is Singapore a morally bad country? We don't know for sure if they would have achieved the same results with a democracy, but in our mental image of "shitty, immoral countires" does Singapore pop into mind?
It's easy to make moralistic claims like this, but to a certain extent we all agree that certain ends to justify certain means. Police shouldn't kill a criminal for stealing an orange. But they probably should kill a criminal if they're holding someone hostage at knifepoint (Purely speaking in terms of the morality of killing people in commission of a crime, I don't know if shooting at a someone holding a hostage is good policing)