There’s actually a fair amount of discord between the Vatican and some of the nuns. There’s a strong social justice component in some subunits of the Catholic Church where they part ways with the Vatican (although I suspect less so with Francis than with Ratzinger, whose resemblance to Palpatine was not a mere coincidence).
Owning shares is actually the method they're using to have standing to sue. It's a shareholder suit. For those curious about which orders, it's a teaching order, a nursing order, a Dominican order (the odd man out), and a franciscian order.