I don't know much about this, and even less about Stuhlinger and Peenemunde in particular, but I suspect that some blame for raining death on people can be laid at the feet of quite a few rocket scientists on both sides of the war, that those scientists possessed a wide range of individual views on the justness of their cause, and that they were nearly all pleased to be able to apply their talents to a good and peaceful cause after the war ended.