True, but that's not displayed as inherent to the Soviets or even unreasonable to a degree. The German brutality is talked about and displayed frequently, and the actions of the Soviets are displayed as a righteous anger in response to an invasion and suffering at the hands of an incredibly evil enemy. War is hell, and I feel that the game demonstrated the brutality of the conflict well. The US and Japan also shown engaging in that same brutality in the Pacific Campaign, so its not something unique to the Soviet missions.

Even then, moments like the one you talk about are rare, and preceded by a lot of context. For example, the scene where the group of SS soldiers attempt to surrender and you have the option to burn or shoot them, comes directly after an entire mission of that SS unit fighting savagely and repeatedly killing captured or surrendered Soviet troops, and then only surrendering because they attempted to escape into the metro system but were cut off and surrounded.

Or even the scene at the beginning of "Their land, their blood", where Rheznov gives you the option of shooting the Germans bleeding out on the floor, comes after those same Germans beat you, a captured soldier, senseless, and were preparing to execute you. Which they were only prevented in doing because of the Red Army's arrival.