So I think from our modern sensibilities, yes she did starve them. But a few things to consider. The society that Myne now lives in isn't our modern one. Allowing these kids to starve is sadly the norm for the church and for society. If she didn't get involved at all they would continue to starve. This is point 1.
Point 2 is that she's also trying to help them better themselves as a whole. Simply feeding everyone would better them hopefully, but she also identified that some simply didn't work at all and expected the same food as everyone since that's how God's Grace works. She instead made sure to establish a sense of trust among everyone that hard word would be rewarded, but not working would not be. She also made sure to call it a reward in receiving food and not a punishment when not receiving food. The goal here seems to be to teach them the value of hard work as well as a potential life skill since her end goal is to have them make paper.
Ethically it's a complicated issue for us now when we consider child labor laws and basic human rights. But the culture is different and she is pushing some of her own beliefs aside to adapt to this culture.
Now none of this makes Myne a saint. I mean, she just wants her books guilt free. But she also is better than the Head Priest who doesn't exactly give a darn about anyone else besides himself.
Just my two copper