I agree with charkan, we might not like what Matilda is saying or the wording choice, but we have to remember the society she's lived her whole life in. In fact, for a medieval peasant woman, she already being incredibly progressive by not forcing Souma to "turn back into a real woman". If not for this being fiction, Souma could've been beaten into submission, immediately publicly outed and shamed, ostracized and labeled insane, or even accused of being a witch and hunted.
For Matilda, her understanding of society is that the men will always naturally be stronger than women because they're the ones doing the hard manual labour out in the forests and fields or, if they're soldiers and knights, waging war and holding almost exclusive rights to wield weapons. Her "need" for Souma to "know the protection of a strong man" is an expression, however terribly and poorly worded for our gender-equality-seeking audience, of her concern for Souma's safety in Matilda's understanding of how the world works. Matilda cares - deeply so - for Souma, and has seen Souma throw herself into multiple very dangerous situations and then displayed no real ability to resolve it once it escalated past diplomacy. Now that there are obvious signs that there are men who CAN do what Souma can't, Matilda's behaviour is her hoping that she can do something, however small, to protect Souma from basically herself.