Birchwood-Casey sells a water based walnut stain in a kit with Tru Oil. I used a Minwax water based stain once, to refinish an old Brazilian gun fitted with some unknown wood. It worked very well, and 10 years later the finish is still nice. I suppose that there may be some brands of stain which could react with Tru Oil, but so long as you stick to a quality brand and a water base you should be good to go.
Sharptail