Communism, as an ideology developed by Marx never endorsed the murder of religious people.

• The abolition of religion as the illusory happiness of the people is the demand for their real happiness. To call on them to give up their illusions about their condition is to call on them to give up a condition that requires illusions. The criticism of religion is, therefore, in embryo, the criticism of that vale of tears of which religion is the halo. - Karl Marx.

• It is clear that the arm of criticism cannot replace the criticism of arms. Material force can only be overthrown by material force, but theory itself becomes a material force when it has seized the masses. - Karl Marx.

• What proves beyond doubt the radicalism of German theory, and thus its practical energy, is that it begins from the resolute positive abolition of religion. The criticism of religion ends with the doctrine that man is the supreme being for man. It ends, therefore, with the categorical imperative to overthrow all those conditions in which man is an abased, enslaved, abandoned, contemptible being - Karl Marx.

• Communism is for us not a state of affairs which is to be established, an ideal to which reality [will] have to adjust itself. We call communism the real movement which abolishes the present state of things. The conditions of this movement result from the premises now in existence. - Karl Marx.

• Communism differs from all previous movements in that it overturns the basis of all earlier relations of production and intercourse, and for the first time consciously treats all natural premises as the creatures of hitherto existing men, strips them of their natural character and subjugates them to the power of the united individuals. - Karl Marx.

• The Communists disdain to conceal their views and aims. They openly declare that their ends can be attained only by the forcible overthrow of all existing social conditions. Let the ruling classes tremble at a Communistic revolution. The proletarians have nothing to lose but their chains. They have a world to win. WORKING MEN OF ALL COUNTRIES, UNITE! - Karl Marx.

• We have no compassion and we ask no compassion from you. When our turn comes, we shall not make excuses for the terror. - Karl Marx.

The abolition of religion is a central tenet of Communism, as expressed here several times by Marx himself. If he didn't outright say that the solution was to kill believers, then his language was at the very least intemperate enough for Lenin, among others, to draw that conclusion. Especially the last one. No compassion, no excuses for the terror? You can't put it much more plainly than that, can you?

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I'm sure that propaganda was used extensively in order to discredit atheism, but again, that's like using Nazism to discredit Christianity — you'd have to be an idiot to fall for it.

And as we've seen again and again here on /r/atheism, the world is full of idiots who have done exactly that. The type of people who say that Stalin killed in the name of atheism.