The broad question you're asking in the subject line and the very specific one you're asking in the body are very different.

To address the very specific one, it would help to know what time period we're talking about and a little more about who your friend's grandmother was and where she would have been. Soviet troops were in Czechoslovakia between March 1945 and December 1945, and then again between August 1968 and 1991. Deaths caused by occupying forces after 1968 are quite well documented, and none of them are even remotely like what your friend described. But there were massacres in Czechoslovakia while the Soviets were there in 1945, mostly committed against the local German population, and mostly by members of the Czechoslovak army, partisans, or self-proclaimed partisan wannabes, rather than members of the Red Army. They were not motivated by hatred for religion, but it's safe to assume that many of the victims would have been Christians.

With regards to the broader question, religious believers were indeed repressed in Czechoslovakia and sometimes targeted for persecution, but they were not massacred indiscriminately.