OK, I've looked again at Digikey and it looks like the caps that are rated for higher AC voltages are film caps. Yes, a lot of ceramic caps are tested at high AC voltage for a small period of time, but most are not rated for continious use over 250VAC. So my question is can a film cap be used in this position? Leads can be bent easily to fit the required spacing as long as the body size will fit.
Yes, the film caps can be used in the circuit.
Following my own concern I asked Vishay through their site about using their DC rated ceramic capacitors. They have pointed me to caution notes in the capacitors' datasheets. It states:
"When sinusiodal or ripple voltage applied to DC Ceramic Disc Capacitors, be sure to maintain the peak-to-peak value or the peak value of the sum of both AC + DC within the rated voltage.
When start or stop applying the voltage, resonance may generate irregular voltage.
When rectangular or Pulse Wave Voltage is applied to DC Ceramic Disc Capacitors, the self-heating generated by the capacitor is higher than the sinusoidal application with the same frequency. The allowable voltage rating for the rectangular or pulse wave corresponds approximately with the allowable voltage of a sinusoidal wave with the double fundamental frequency.
The allowable voltage varies, depending on the voltage and the waveform.
Diagrams of the limiting values are available for each capacitor series on request.
...
During operation in a high-frequency circuit or a pulse signal circuit, the capacitor itself generate heat due to dielectric losses.
Applied voltage should be the load such as self-generated heat is within 20 °C on the condition of environmental temperature 25 °C."
It means that for the secondary the capacitor should withstand not less than 550V*sqrt(2)*2~1555V. Then the 2kV is not conservative voltage, but a must!
The Vishay support (following my requested environment) suggested S103M69Z5UP63K7R (digikey part #1256PH-ND) as the best substitution for the missed capacitor.
I've looked through other candidates and found similar capacitor DEBF33D103ZA3B from Murata (digikey part #490-4254-ND).
Both capacitors have lead spacing 7.5mm (as on the PCB).