How many Soviet citizens died at the hands of the Nazis? Far more than died hands of the Soviets. The Soviets did nothing to the Nazis that wasn't done to them. The Nazis spent three years torturing, starving and mass murdering the Russian people. It's only right the the Mazis got a taste of their own medicine.
Many examples can be used when arguing for why civilians must be considered as illegitimate targets; some more effective than others. My rationality for why attacking civilians is wrong — without getting into moral concerns — is done on the dangers of allowing such an action: retaliatory actions, making peace difficult to reach, post-war cooperation difficult, increasing the chance for future wars and a heightening of the terrors and human cost of war. The hurtful actions of either side against civilians during WW2 was objectionable and can't be justified, to justify them is to wilfully increase future repetitions. Not even the bombings of Hiroshima and Nagasaki could be justified, but that's another topic.
No, It was not right that the Soviets killed thousands of innocent German citizens when they invaded Berlin. However, it happened and there is nothing we can do about it now. Although, I do feel that they could have obtained the same result without having to kill all the innocent people and bystanders.
No, in times of warfare, civilians are not priority targets. Better targets include missile sites and military bases. Civilians are not acceptable targets under the treaties of the Geneva Convention due to this type of attack. Although Nazi Germany was a despicable power, not all of its citizens were guilty of horrific crimes. Killing unarmed men, women, and children is never ok.