Sam,
Whatever you do to it, you really need to organize those cables so is doesn't look like you're transporting a nest of snakes.
Unless that bike is worth a whole bunch of money, go ahead and paint it. Consider the effect of cable colors when you make the choice, as they might not leave you with too many options.
Also, changing out the rims truly isn't that big a deal. Take some good before pictures just in case, but truly, with a couple hours and a set of directions from Sheldon's site, you'll have some very respectably straight wheels on your bike.