In my opinion, "ish."
Let's say you have a church, and there are two branches to it. One is the branch that goes forth and feeds and heals people, defends the weak, and other good things. The other branch contains the bureaucratic side that includes an inquisition that tortures people until they confess to their crimes, then likely kills them messily. (There are likely more branches than this; we're dealing with these two). The first branch is almost certainly Good. The second branch is almost certainly Evil.
The reason I'm saying "almost certainly" here is depends entirely on what the crime is and who knows about the torture. If the crime is not going to church every week, or associating with haflings because the church has declared Small races to be unholy, or stuff like that, then this branch is pretty Evil. They're hurting people for things that are only crimes because the church has said so, not because the actions are actually harmful.
If the crime is "consorting with demons of disease and misfortune in order to gain powers to hurt people you don't like," then the branch is evil (for using torture) but not necessarily Evil, in the grand alignment sense. However, they probably also wouldn't be good, either. They'd be more Neutral--they're doing some awful things for the greater good. It's a dirty job, but somebody's got to do it. It would also depend on how much non-torture investigation they did before hand, of course. Grabbing people because their neighbors turned them in would be more Evil, while doing careful research in order to make sure that they only get the actual guilty parties would be more Good.
But, if the crimes (of viewing Small races as anathema, etc.) were edicts handed down from on high--by the literal gods--then I would view the entire religion as being Not Good. The church might be Neutral or Evil, but with a Good branch that heals and feeds the needy. Especially if that Good branch also helps out Small races on the qt. (This is where schisms appear)
If the prohibition about Small races was due to some high priest's personal dislikes that just got codified into not-actually-canon law, or because there once was a war with some Small races and anti-Small sentiment got brought into the church, or the halfling-hating ruler of the land demanded their dislike be made into law, under pain of having the church dismantled and the priests gruesomely murdered, then the church isn't necessarily Evil, because it was outside interference that corrupted them. They could well be on their way to becoming Evil, though, if the corruption isn't stopped before it becomes endemic.
You might find the Safiqi complicated then.
In setting, the vast majority of Safiqi sects (which usually revere specific facets of the One, an idea inspired by the various names of God in Islam) are extremely "serve the people" oriented. E.g. some devotees of the Unknown Knower contribute to public education and aiding the poor (people who "go unseen" as it were), those of the Soothing Flame often provide healing and shelter to others in need especially in crisis situations, the Temple Knights are generally dedicated to the Stalwart Soldier and defense of all ordinary folk across the realm, the somewhat rarer devotees of the Resolute Seeker hunt down legit nasty monsters (like the aforementioned
nasnas or basilisks) that live out in the desert and plague the world, etc.
And then there are the Asiad al-Khafyun. A group that can best be described as the secretive "internal police" of the Safiqi. They have three main purposes: (1) hunt down and either capture or, if necessary, kill any heretic priests who have abused their powers, especially if that abuse comes in the form of controlling or dominating others, (2) eliminating extremely dangerous interplanar threats to the world (more on this in a bit), and (3) keeping an extremely high security vault of heretical or dangerous knowledge/artifacts/entities, so long as they can be safely contained and examined.
They have done some things in the past that might qualify as "evil" in your eyes. For example, those extraplanar threats I mentioned? Yeah until very recently (because the player characters happened to it) one of those threats was a literal infectious mind-virus spirit of decay and savagery that can literally warp reality in areas where it has grown strong. It was called the Song of Thorns, and exposure to it in written, sung, or physical form, even only small parts of said written or sung form, could infect a person and cause the Song to spread. Prior to the party getting involved, the only progress in opposing it that the Safiqi had made was a magical form of suppression that would allow them to examine the infected without risk of becoming infected themselves....and that magic was very old. As far as they knew the only way to deal with infection was to kill the infected (which, with the tools available to them, was true), and to purge all references to it and instances of it. They had literally
erased a city from all records (Al-Taraf, which they now call the Lost City; legitimately most people have no idea it ever existed) in order to keep the Song secret, because a massive outbreak occurred there and they weren't able to save it. They have killed people solely to keep this secret safe, because it is extremely easy to get to the realm where the Song of Thorns once ruled (though it can be hard to get back out again), and even one infected person getting out could cause an uncontrollable infection of the whole world.
Other than their stuff dealing with the Song though, they're almost entirely focused on policing the Safiqi themselves, and because of the seriousness of this charge they undergo some pretty painful initiation rites which bind them to a certain code of conduct. It's complicated and I haven't nailed down all the details but basically they have ways of magically enforcing adherence to the rules they enforce which the highest echelons of the priesthood could use against them should they go rogue (which is a big concern, because a portion of the very very early Asiad al-Khafyun DID go rogue!) It's a very select group and membership is for life; once you join, you never leave, and you become part of more or less a divine "assassin/ninja" group dedicated to eliminating threats that are difficult or impossible for ordinary folk to deal with. So the vast majority of their effort is spent on hunting down wicked priests who abuse their cleric magic to hurt people, create undead, or otherwise do blasphemous and overtly dangerous/harmful things. They also cooperate with the Temple Knights in dealing with more ordinary "evil cult" type stuff, but that's not really a core focus.
Their current leader is Fahd el-Sattar. He is an
extremely serious man (very few non-serious people would ever consider joining the Asiad al-Khafyun), but the party has earned his complete respect with their tireless efforts to aid them against various threats and, in particular, their total defeat of the Song of Thorns. (Though some of that was because he could tell instantly that a party member had had some kind of interaction with the One personally, which...yeah for a man of deep faith that's pretty obviously going to earn some immediate and pervasive respect.) The party considers him a formidable man and an ally to call on sparingly, but an ally nonetheless.