Since you are using the ArcadeVGA card, it already outputs 15Khz sync signal. What I don't know is how your VGA to Scart cable is buildt. The gfx-card outputs 5 volts on the h and v sync so there must be at least one resistor there to get the voltage down (since the scart has 75 ohm impedance this can be done). In your cable there must also be some circuit to combine the h and v sync to composite sync. Many ways to Rome. Connecting them together (and a resistor) could be done since you are using the ArcadeVGA card that outputs both h and v sync negative. Another way is to use diodes. The best and most reliable way is to use an xor gate that outputs negative composite sync no matter what polarity you put into it.
Anyway, since you are already using a vga to scart cable that works it must produce a composite sync signal some way or the other. All you need to do to connect you GunCon's yellow plug to your composite sync (center) and ground pin on your scart plug. I don't rembember at the moment which pin number this is, just that you should use the same pins that comes from the gfx-card (after the sync combine circuit) via the cable (sync ones) and not the output pins on the scart plug. (There are both input and output pins.) The impedance in the gun is so high that it won't steal any voltage. But if you cable uses a resistor to drop the voltage, disconnecting the scart plug from the TV would result in feeding the gun with 5V. I think it can handle that, but don blame me if it doesn't.

Split a phono extension cord and connect that so you won't have to cut you GunCon's cable.
Just remember that different resolutions (refresh rates etc.) may need different calibration. Try sticking to one res for guncon games. It should work great if you can handle the calibration routine.