Changing store currency from a plugin
In your plugin have you tried updating the currency and paymentCurrency fields in the craft_commerce_orders database table?

Depending on when you want to set the currency and how you are determining it, you could either do this by a direct database query, or modify the values in the order model before it is saved using this hook: https://craftcommerce.com/docs/events-reference#commerce_orders.onbeforesaveorder