This is a good idea. Also, a number of places will bring you a bento with some of the side dishes that your wife won't eat. You can eat those while she eats the rest. Just make sure beforehand that the main dish is something she will eat, like cooked fish.

If you are a big fan of sushi/sashimi, do not even think of taking her to a good sushi place. There will be nothing for her to eat, except cooked eggs and cucumber rolls. In some places the chef will be personally insulted if you reject his food, and you may want to avoid that.

A lot of places (for example, izakayas and regular restaurants) will also offer sashimi in addition to other things, but that's not the prime stuff. Edible to very good, but rarely for the connoisseur, except at high-end kaseiki or kappo places, which you rightly point out should avoid. At those high-end places substitutions could be considered an insult, since the order, arrangement, and choice of food follows a particular pattern that somebody spent hours fretting over, and you do not want to upset the wa that way. The unscripted agreement is that you will be taken care of, and you are to be grateful for the care you are being given. Making ripples in the water is not appreciated.

If you are big sushi fan, you may want to have the talk with your wife. This is the talk my mother and father had. My mom doesn't really go for raw fish and shellfish, while my dad just loves it, it is probably his favorite food. So the talk was one where my dad told my mom that one night during their trip my mom would have to find herself a place to eat, because he was eating sushi, come hell or high water. They horse traded something, don't remember, but it was along the lines of "then tomorrow we go to the Ginza to look at kimono silks to make a dress for your daughter's wedding" or something like that.

The downside of this is that you may not want to eat sushi anywhere else after that.