Walt Being the stubborn guy I am, I still think that it wouldn't be too difficult to work with lenses - for example, you could make all the lenses refract at a fixed angle, and make sure the player has access to a mirror that reflects at exactly that angle too. If the lens always refracts at 30 degrees, and the player has 30 degree mirrors, then you don't have to worry so much about very fine control because the mirrors and lenses match perfectly every time.
Example of the kind of lens I mean (which is technically called a prism!):

I especially love the idea of using your own mirrors/lenses to interact with enemy ion beams (for example, you could reflect an opponent's ion beam right back at him, or accidentally reflect it at one of your allies), and I think that would be a really cool thing to have in the game. The ability to reflect and refract your enemy's ions is a lot of the reason why I'm so attached to the idea of mirrors and lenses.
That being said, if it's too complicated it's too complicated. I also really like the idea of on-the-fly rotation, and I think that'll be really cool to have if you decide to do prisms only. Thanks for taking the time to read and respond!