Sigh...this is a bad thing that is extremely rooted in asian culture, if someone is a criminal their close family is associated with their evildoing, even if the person itself was unrelated.
Family of a criminal being harassed simply for being conencted by blood even if without having meet for years can be enough to be isolated from the community or even fired from a job.
I'm guessing is associated to a old belief that anyone that had commited crime was tainted and anything they touched was tainted too, so their kids would of course being branded too.
This girl thinking for a second that MC would treat the son of a criminal like if they did the crime is proof she doesn't believe in him if anything, from what I read it doesn't look like he would treat her badly for it.
And even if he was that type of person before I doubt he would be now.
We need more information though, she is the daughter of a criminal, MC took her under his wing when she was alone, her uncle was powerful but abandoned her, so I presume MC didn't knew about the criminal and it was discovered after he got isekaied, or is bad writing and MC already knew, her uncle abandoned her for it and took her his office only after MC trained her, she was powerful and if MC returned she would have disappeared, good planning.