First, her initial writing was apparently in Urdu, starting when she was ten or eleven. That's plenty old enough to write in your own language. That's also the age when English becomes more prominent in education generally.
You need to understand the social stratification in the subcontinent - I think it's the same in India as well as Pakistan. For the middle and upper middle classes, which Malala's family definitely belongs to, knowledge of English is a prized possession. We get sent to schools where the medium of instruction is English, even as we learn our mother tongue at home, or as a second language at school. Many of us are bilingual, quite a few even trilingual, and most of us are more comfortable writing in English. Don't forget, her father is a school principal - hardly a case of an illiterate tribesman's daughter.
Let's not try to create false equivalence - shooting a thirteen year old for saying something you don't like is still shooting a thirteen year old for saying something you don't like. Whatever other issues there are, the Taliban have once more revealed themselves to be a bunch of craven assholes who can only bully people into submission, not debate with them. There may be other issues with her backing or funding, but no conspiracy by any theory ever justifies shooting a child in cold blood.