The Soviets used the Kremlin and its churches as a seat of power during the government. Many were still valued as historic buildings and were converted or kept as is.

I think there is a slight misinterpretation being made here though. The Church of Christ the Savoir was not destroyed because of anti-religious reasons, although they may have played a part in the decision, rather it was destroyed because of plans to build a new capital building for the Soviet Union. The Soviet Government wanted to move from the Kremlin to a new grandoise capital building known simply as "The Palace of the Soviets." It was to be built exactly where the Church of Christ the Savior, and in fact the foots and initial steel was placed at the onset of World War 2. However due to the costs of war the building was never completed, and subsequent governments did not continue the plans to build the Palace after Stalin's death.

To my knowledge it was never a plan to destroy any of the Kremlin's buildings because of the significant cultural history of the area, instead the Soviets re-purposed many of the buildings to their own means throughout the Soviet Union.