Yeah except a lot of those games were designed for the wiimote, so by using something else you are actually playing them wrong. Games like the resident evil chronicles' in particular just won't work with a normal light gun.
I'm not sure what you mean by "playing it wrong"?
The Wii remote outputs like an analog controller. Any of my PC guns which output as analog controllers in Windows (which is most of them) work well in Dolphin.
The type of controller is not important in Dolphin though as it takes whatever controls you choose and then emulates a Wii remote. The Wii remote is just a pointing device with buttons. It doesn't matter if you use an absolute mouse gun, a regular relative mouse, an absolute analog gun or relative analog controller. You choose whatever you like to play with. It has excellent fine tuning options too.
Every function of a Wii remote and nunchuk can be allocated to any controller or combination of controllers. If a game needed an accelerometer and/or a gyro as well as a pointing device, you can add what you need.
Hybrid light gun / FPS games like Resident Evil Darkside Chronicles which have you walking around while shooting also benefit from Dolphins flexibility. It lets you use a far more accurate gun to aim and then assign movement to any other controller including a real Wii nunchuk or PS Move controller. Or you could even plug in an Apac and hook up a real Gun Survivor 2 arcade gun which has linear pots on the gun for moving.
Every PC gun I've tried worked at least as well as a Wii remote. Most worked a good deal better though as the Wii remote is not great as a gun. More accuracy, more flexibility and being able to sit as close to the screen as you like improves every Wii gun game imo.
I should add that I enjoy the Wii and it's remote for a lot of it's games. Just not light gun and FPS games. I'm certainly not anti-Wii. Games like Star Wars the Force Unleashed are better on the Wii than the PS3 because of the Wii remote. I hook up a real Wii remote and Nunchuk for my Son to play games in Dolphin sometimes.