Both terms were invented and popularized as a derogatory term by those with social power to denigrate and marginalize a potential challenger. They serve as an inoculation in the brain against the messenger of change. The instant the messenger starts talking, these memes spring forth to shut down the brain from listening. "This is just another one of those damned uppity niggers/militant atheists who doesn't know his place."
What is needed to impliment this type of tactic is a dominant social group with an interest in preserving its status who read each others' work, and who have the ability to use a particular term over and over again before various audiences. We do not need anybody making a plan in a back room somewhere. One person uses the term. Others like it (because they feel that it will be effective in preserving their status), so they adopt it, and the term spreads.
An important feature in both of these terms is that they are both descriptive and prescriptive - or, more precisely, pejorative. They are used to generate in the agent an immediate emotional reaction - a feeling of contempt - for those members of the target group that dare to challenge the status quo.
These emotional associations are important. They help to control the thinking of those afflicted with these memes. they help to make the brain unreceptive to the challenger's message.
It also likely worked, at least in some cases. To intimidate blacks against standing up to the injustices of their day. These moral rituals not only generate a feeling of contempt in white people so that they could more easily swat aside calls for equality. They also infected the brains of African Americans - those who wanted to be seen as good people - praised and admired by their community. These are human interests - and they generate a certain amount of discomfort over any actions that might earn one the derogatory label, "uppity nigger" (or "militant atheist" in the parallel case).
Unfortunately, the human interest in social approval has its drawbacks when the society contains inequality and injustice. In those cases, one has to be a champion of inequality and injustice to acquire that praise and will be condemned for challenging it.
Indeed, we find in our history blacks who were just as adamant in criticizing the "uppity nigger" as the whites - using the same derogatory terms and, furthermore, using substantially the same types of arguments we hear today in the atheist community. You are the reason that they hate us. It's all your fault. If we could provide them with a kinder and gentler message, they will no longer see us as a threat. They will come to see us as good people and then happily gift to us political and social equality.
There are two problems with this argument.
First, justice is not to be asked for as a gift, it is to be demanded as a right. Treating it as a gift implies that others have a legitimate authority either to give it away, or to refuse to do so - as they please.
Second, in an unjust society, all strategies for ending that injustice, be they accomodationist or demanding, are a threat. They are a threat simply in virtue of the fact that they seek to end that status of privilege. If one of them appears less threatening than the other, it is probably in virtue of the fact that one accepts, rather than opposes, the current social order - so it is not a threat.
In the case of the "uppity nigger", this tactic has been effectively challenged - for the most part. We will hear about the "uppity nigger" and the "militant atheist" until the end of time. But the term will be endorsed in smaller and smaller communities.
The counter-tactic, as it turns out, was to speak the truth. The counter-tactic identified those who used the term as bigots prone to making unfounded derogatory accusations whose primary purpose was to preserve a culture of - to be honest - white supremacy. As this fact became more widely known, the use of the term faded and lost its social appeal.
I would suggest using a similar tactic against the "militant atheist" meme. It is, as I said above, a term invented by those with social power for the purpose of marginalizing and denigrating those who challenge their supremacy. The use of such a term (except in certain contexts by members of the target group themselves) identifies the user as a bigot seeking to preserve a system of injustice by promoting a social aversion to the members of the target group.