I can't post the link I want, because the URL has a swear in it, but google the words "intent" and "magic," and read the first article to come up.
Now, I'm not actually as frustrated, upset or offended as that article would suggest (so, if the snarktastic tone offends you, it isn't my fault, because it was never my intent for you to get offended.)
The basic point is that everybody who understands the words "done in the name of X," understands them to mean that something was done for the primary purpose of supporting X, and with X as the primary motivation. The simple action of arguing "Stalin killed in the name of atheism," regardless of what you intend it to mean, encourages people to see Stalin as a Crusader for atheism-- a person who decided that there was no god and, based on that idea, decided to form a tyrannical government founded on the idea that there is no god, and killing all who disagree, solely or primarily for the purpose of evangelizing the atheist position.
Maybe it's not what you mean, but intent isn't magic. It's what you said, and continue to say, and continue to argue, and thus, what you encourage other people to believe. Which, end result, makes the world less safe for atheists, because it bolsters people's views that atheists are dangerous and, us being a minority, we're unable to counter such views as quickly as they are able to spread.
The position you've taken is neither simple nor base. You're arguing that you don't actually believe what you're arguing; and demanding that people believe that you're arguing what you want them to believe you're arguing, instead of what you are actually arguing. If you don't actually believe what you're saying (I described what you're saying, above), then please find words that mean what you believe, instead of trying to simultaneously argue a position, and change our society's understanding of what certain words mean, just so that you can continue to use a turn of phrase you like, even though it doesn't mean what you want it to mean.
Because as long as you keep saying what you're saying, people will keep believing that you're saying something that you claim you don't believe.