There are many Jewish and Muslim defenders of exemptions for ritual slaughter who say that what they are doing is ethical, a claim for which they offer two basic reasons.
The first is the argument that the animals do not really suffer more during the ritual slaughter than they do through other means of killing. This may be true and if it is, then there would appear to be little reason to condemn or ban those rituals on ethical grounds. However, this may not be true, and in fact there are some good reasons to think that it isn't.
That is a technical question which has little to do with religion. More interesting and relevant here is the question of what we do if the animals do indeed suffer more when slaughtered according to traditional religious rituals. Here, defenders of religious tradition make their second argument, which is that we are dealing with "fundamental religious practices" and any attempt to ban them would constitute unethical "religious discrimination."
Ergo, the exemptions given to religious groups should be maintained regardless of whether the animals suffer more or not. Since this is likely the position of any of the defenders if it could be proven that animals suffer more, it would probably be more honest for them to ignore the first argument and focus instead on this it is, after all, the only argument that applies in all situations.
It is unlikely that this argument would ultimately prove persuasive. Granted, it would create a difficult imposition and would prevent them from following what they believe are very important religious obligations. We have already established, though, that when it comes to extreme situations that society finds morally abhorrent, religions are not and should not be exempt.
This is the case with human sacrifices, so the question we need to ask is if the ritual slaughter of animals qualifies as a situation extreme enough to outlaw anyone doing it, no matter how strongly they believe that they should. Currently that probably isn't the case, considering the status of animals in society.
On the other hand, society is moving in a direction where that might become the case in the future. The ritual slaughter of animals under halal and kosher rules is a better candidate for being outlawed than many other things because it does involve unnecessary suffering. This makes it quite unlike things such as drinking wine at communion or wearing religious headcoverings, two religious traditions which may conceivably be the target of criminalization.
Religious ethics are not always the best ethics sometimes religious dogmas sanction or even require behavior which is morally dubious at best. Although devout religious adherents may sincerely believe that certain behavior is required of them, that does not necessarily mean that that behavior must be permitted and if it happens to be innocuous enough to permit, then it should be permitted of everyone, not simply a few.
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