There's that.
In Galgados, pulling some weirdness will get people worried and nervous...but if they decide that you're on the good side (not necessarily the CHURCH side, just not a bad person), they'll be relatively cool with it (though not 'at ease', like in D&D worlds where people take magic as almost a matter of course...which, honestly, is a tad ridiculous unless you're IN a D&D world, where there are tons of mages, mage schools, etc).
In Kushistan, using magic in a non-world-conquering fashion might get you a job.
In Togarni, it'll either get you a job, or killed if you turn said job down (not because you're 'using magic', but because 'you're using magic and not supporting Mr. M. Gaul).
In Alberia, it'll get you revered.
In Itzi, people will flock to you for survival (if you're at all benevolent).
In Daphne, if you're a women you'll be hired into their Special Forces (secretly). If you're a man, you'll probably get hoofed out of the country.
And in Pristinia, nobody -- not even the local Inquisitor (there is only one) -- will even care (I mean, if you're attacking people with it, they'll react poorly, but that's more because "attacking people" rather than "attacking people with magic, specifically"). The Inquisitor will invite you over for a beer, really, and toss a few questions your way to see if you're the kind of person he needs to deal with or just ignore while he sits on his porch, whittling and waiting for an actual supernatural THREAT. At which point he'll probably ask the locals (read: non-human, magic-using beings) for assistance taking care of it.
Etc.
Really, the business about 'No Fun Allowed Factions' with regards to the Inquisition is a perfectly natural reaction from a good chunk of the world that seriously suffered under magic for a bloody long time. Yeah, some of it was manipulated by the second level faction, but a lot of it is derived from a (very realistic) perspective that 'Magic allowed a tiny bit of the population to utterly control and enslave a big part of the population, and if you didn't have magic you were dirt', as well as the idea that 'Guy goes power-hungry or bonkers with a sword, he's a threat to stuff in arm's reach; guy goes power-hungry or bonkers with supernatural abilities, he annihilates cities'. It's also not a completely ubiquitous perspective; as Beadle says, there are LOADS of places where players can cut loose more safely.
It fits with the setting, as presented.
What comes next in this post I'll preface as my own opinion, and mileage may vary. ^_^
I've always found the business of how magic is viewed in 'standard D&D worlds' to be utterly unrealistic and somewhat banal; it's great for worlds where the entire point is 'adventure, kill things and take their stuff', but once one gets into the complexities of actual intrigue, politics, rulership, social classes, etc...it becomes somewhat odd that the 90% of the population in the D&D worlds aren't either scared crapless of their magic-types, or utterly enslaved by them.
Granted, there's always the business of 'gods don't allow it', or 'pantheons look down on it so the Churches prevent it', or 'saccharinely-good (and poorly-dressed) Elven rulers stamp down on such things'*, or 'Powerful Epic-level NPC's of various forms of Goodness run the Good Countries', but those are pretty heavy-handed things as well, really.
Basically, for me many D&D games/settings seem to run 'There are checks and balances on all of the NPC's, but the players can go hog-wild.' Anima says 'Yeah, the setting treats everyone the same -- NOBODY is allowed to go hog-wild, one needs to find a more tricky way to pull it off.'
Second-level group of shadowy controllers in Anima, yeah, they're 'everywhere'...while simultaneously specifically noted as 'never really will do anything, unless the entire world is threatened or the OTHER shadowy controllers stick their faces into a situation'. I mean, if one looks at the Wars in the Shadows, detailed rather impressively in Gaia Book II, there was a grand total of ONE terribly massive war that Imperium stuck its nose into over the course of about 1000 years (the Baal situation). They didn't even GET involved in the War of God, which sprang from one of their monumental screw-ups, until (again) Rah's temper tantrum threatened to annihilate the entire world.
They don't do anything, really (beyond 'will stop the players from blowing up the planet, should they ever reach that level' and 'this particular arm of their organization will stop everyone from just magically making money and crapping on the economy'). They're there as setting background. I rather like it, but mileage varies.
And when I say 'destroy the world', I'm not talking about 'mankind wars upon itself and nearly destroys itself completely' (been done, they didn't show), or 'A sleeper awakens and annihilates the current culture and empire, sending everyone back to the stone age' (they would take notes, nod heads, and say 'Interesting'). I'm talking 'the world itself is about to be rendered completely sterile of life, no comebacks'.
Now, if that is what players want to do -- sterilize the entire world (or, I guess, make their own money with magic, and if they can't do that I have the World's Smallest Violin™ to play, just for them ) -- then I would suggest they keep the heck out of my games. ^_^ And I don't need a villain who's looking to eliminate everything as a challenge in my games; there's plenty I can do that's far more interesting than that kind of 'Ultimate Evil' thing (there are better, more complex and interesting forms of Ultimate Evil...).
I guess players might get miffed that they can't be the Strongest People Around™; I've never felt that to be important, myself.
* at this point, I'll note that the 'elves' of Anima - the Sylvain - have a history of either being hands-off when it comes to other cultures doing awful things (as long as it doesn't impinge on their civilization), or (on occasion) indulging in genocide against things they don't like. For beings of 'the light', they can be awfully heavy-handed...but then, Anima DOES also make the point that 'the light' isn't necessarily 'good and nice' (just look at some of the Beryls for examples of that, and their actions).