To me "to be charged of" is a more permanent situation, whereas with "charged with" she was "encarregada" in a more ad hoc way (say, everyone comes to a place and everyone is assigned a task - she was charged with the kitchen.) It even mean "to be responsible for something", but I would think it as task-wise.
I am afraid (be) "in charge of" is good wording to our currently examples, charged with is okay, but I would drop "charged of
" (it could make confusion with "charged of some demeanor or crime, etc).
"To be in charge o
f" is an expression, not a verb per se, and it´s understood as a noun (the one who is in charge = the one in charge
of) so I am not going to say it´s transitive or not. It´s not a verb in such case, albeit the word "charge" is in the sentence.https://simple.wiktionary.org/wiki/charge