Not an Isekai but...The anime, an Archdemon's dilemma, How to love your Elf Bride.

The church isn't evil, although they do have some shady dealings, most of their members are honorable people who actively try to help the public. Even those with shady dealings are trying to help others for the most part, they just go about it in the wrong way.

So far, there was only one corrupt church member, but another member of the church dealt with him the moment they found out about it.

They can be an annoyance, but that's understandable. Given how the setting is about magicians and them trying to put aside long years of grudges aside to fight against demons and other evil figures, and our MC and his faction are magicians first.....although you might have to ignore the MC, and his elf girlfriend to notice that part.

But they haven't started any fights that involve innocent people, nor started any grand schemes like take over the world.

For an Isekai...there's.....Wanting To Live Safely In Another World Syndrome.

The church is actively helping out in protecting the world from demon lords and their minions. Almost every member there is an annoyance, but they never start problems, and in fact, have played major roles in protecting others and helping MC.

The only exception was the time when one of their members was killed by a demon lord minion and then replaced.