The easy, in universe explanation, is that whatever her family was doing by focusing it's everything on insects was more successful than most people would have had a chance to realize and they got closer to True Magic than expected. Remember that Emiya knows about the True Magics, and should have some level of personal experience with the Second and Third. Her having a special and unique Magecraft that lets her include phantasmals in her domain doesn't first mean "suspicion of being a threat to all mankind," but "her family might be in the running for Sixth."
Honestly my thoughts are the opposite. Not something like "she's a threat to mankind" but more of "Huh, I wonder what her magecraft is like. But I probably wouldn't get the explanation even if she told me about her Mysteries." Because it's worth pointing out that Emiya Shirou, both the boy and the Counter Guardian, has a canonically very skewed understanding of what common Magecraft is like. As opposed to the usual hypercompetent versions you see of him in fanfics, even as an adult, Emiya Shirou never really got an in-depth study of what Magecraft is like, only what he learned from Kiritsugu's terrible teachings and from Rin's tutoring later in life. And he was never really Waver's student, more like student-adjacent.
He can't really grasp the true extent of how weird Taylor's ability to control entire swarms of insects because unlike Lord El Melloi the 2nd, he just doesn't have the academic and magical background to. Sure, he has experience with what
Servants can normally do with Unlimited Blade Works, but not what
Magi can normally do if you get my gist. He's aware that Taylor's power is weird, but cannot appreciate just how weird.
To be fair, there aren't a lot of modern day magus families that we know of that don't go hard into suspicious territory. Remember that the goal of almost literally every modern family is to reach the Root and get themselves some of that nice True Magic, and some families are closer than others.
Also, to be fair, what we know of Magus families
is generally skewed towards the suspicious sorts as well. I know it's a stereotype that Nasuverse Magi are all backstabbing monsters that would sacrifice their children if that got them to the Root, but we actually do have examples of Magi in multiple works that would find that kind of thing abhorrent. I mean, it was mostly because of Toole's efforts, but Goredolf's family is very moralistic for example.
The thing is, nice Magi families like that don't really get story attention because, well, if they're doing nothing bad then the protagonists of the various works won't have to step in and fix their messes. I'm sure that there's plenty of Magecraft users just quietly improving on their family craft and doing nothing bad all around.