Spiritual directors back in the day were just as leery of people getting anorexia as a spiritual director today would be. Spiritual directors often ordered people to eat, and even to fatten up. The mission people where Kateri went were very well-trained guys, and would have done this if they’d thought she were starving herself.
You will read on the website that, since Iroquois and Algonquin spiritual life included a lot of mortifications already (either to “make yourself strong”, or to bring the attention of good spirits who would feel sorry for you and give you visions and power), the good priests at the mission did a lot of riding herd on over-enthusiastic converts!
But there’s nothing wrong with asceticism, per se. Training hard isn’t wrong for spiritual life, any more than it’s wrong for someone heading for the Olympics. Doing penance for your own sins and the sins of others is constructive and helpful. Since Kateri couldn’t do the heavy work for the village, she probably felt that doing heavy prayer work was how she could contribute, as well as doing it from love of God.
Also, you will read that after she got to the Christian village, Kateri partnered up with an older married woman who was devout like her, and who treated her like a daughter. She helped the priests keep an eye on her. She did extraordinary penances, but nothing beyond her strength. When she got too harsh, the priests told her to pull back.
It was a hard time, and a lot of people died young. It seems pretty clear that someone frail like Kateri would not have lived long in any case, when so many strong and healthy people were dropping like flies. But she made the most of her time as best she could.
