Sorry, but according to a Malawi stats site,
Female Genital Mutilation (FGM): A few small ethnic groups practice female genital mutilation About 18% of females undergo this practice.
That's a far cry from 90% and it's still an accusation unless you can prove it.
Work on reading comprehension. Start by re-reading the sentence which mentions only one country (Ethiopia) and gives the rate THERE as 90%. I chose Ethiopia as an example of the lack of correlation between religious affiliation and female genital mutilation, since I was responding to your question: "Do Christians mutilate women?".
Malawi seems to have a lower rate than many countries in that part of the world, but in a country where the practice isn't so widespread as to be the "norm", it's likely to be the poorest, least educated people who are practicing it, so there's more than 18% chance that this baby's mother had undergone it (at least if the father's claim to be unable to afford to feed the child is true).