With all due respect, I think the weakness of your position is that you are looking at actions divorced from intentions and/or consequences and making moral judgments regarding those actions. This has always been the weakness of pragmatic ethical systems like deontology, as you rightly note. However, There are at least two other major branches of ethics which haven't fully been explored here (at least to my knowledge).
Utilitarian Ethics is the position that the outcome of an action is the central concern of ethics, and the goal should be to cultivate as much "good" as possible for as many people as possible. Now, there are dozens of different forms of Utilitarian Ethics, but they all basically attempt this above point. The advantage of this position is that it avoids the problems you mention, as the outcome is the focus, not the action. So, using your cavity search example, there is a logical reason in Utilitarian Ethics that rape is different than a cavity search; the former causes immense suffering for no benefit to the sufferer, while the latter benefits the sufferer in that there are reduced quantities of deadly weapons present, and therefore, the person is safer, as well as reduced quantities of contraband that is often the cause of violence in settings where cavity searches are more common. This good outweighs the bad of the cavity search. However, there is a significant weakness. If a person is gang raped by enough people, eventually, he or she will loose consciousness and/or die, and the number of subsequent attacks becomes irrelevant. The damage has been done, and whether the victim is assaulted by 3 or 300 more is virtually irrelevant. However, the attackers are deriving some pleasure from the attack, and if you add enough attackers into the mix, it is hard to overcome the argument that their pleasure outweighs the victims' pain. To put it another way, if the pain of gang rape until death is a -100, and the pleasure each attacker derives from the attack is 0.5, then, once the 201st attacker is done, the situation becomes a net positive. And, if it is a net positive, according to Utilitarian Ethics, it is morally right. Now, I am reasonable sure that we all would argue that gang rape can never be morally right, but one would be hard pressed to establish why under Utilitarian Ethics. Hence, as a theory, I think it is lacking.
In contrast, Virtue Ethics is the position that things are right or wrong based on what sort of people we are or become based on what we do. In other words, why we do what we do is just as significant as what we do, and both add up to develop our moral character. So, going back to the cavity search, few people who perform them actually want to, and they only do it because they believe the prison system is safer and better without the contraband smuggled in orifices. Further, rape is the violent dehumanization of a person for the sake of selfish pleasure, whereas cavity searches are in the best interest of the prison society (or so it is believed, anyway). Therefore, one action is selfish, and the other is selfless. Should a guard take sadistic pleasure in performing these checks, that person is not exhibiting a virtue, but a vice, and therefore is morally wrong, even though the actions haven't changed. However, the weakness of this position is there are often contrasting virtues in a given situation. Assuming the virtues of honesty and protection of those in mortal danger, it could be difficult to work out the proper moral action/attitude when a murderer asks you where his victim, who just ran by and hid, went. Personally, I think this issue can be resolved if virtue is seen as singular gem with myriad facets, but that is a conversation for another time.
So, all this to say, the subject of ethics is vastly more complicated than is commonly portrayed, and only one major branch of ethical theory is primarily concerned with an action itself. And, to address the OP, much of it will depend on what sort of ethical system is adopted and what field of study is the basis for this. If it is a scientific based utilitarianism, they may see the proliferation of religion as ghastly, as it (in their minds) only creates false hopes and interferes with our progress as a species. If it is a religious utilitarianism, they may see our lack of forced conversion as ghastly, as this may ensure the condemnation of millions (assuming, of course, that they believe that forced conversion is legitimate conversion).
(For anyone who may be interested in more information on these, this [
Virtue Ethics (Stanford Encyclopedia of Philosophy)] and this [
Consequentialism (Stanford Encyclopedia of Philosophy)] provide good introductions on the subjects)