I have never had a reliability problem with 339 outputs discharging similar sized capacitors, but you are right to address the potential issue, especially if it comes up in a datasheet audit of the design.
Anything in series with pins 1 and 14 will have no effect on the charge-up time constant. Also, while an extra 100 ohms or 1K will create a voltage divider that increases the minimum voltage across the capacitors in the discharged state, that increase will be approx. 0.33%. This voltage increase effectively shortens the charge-up time constant to a trip-point value, but probably not enough to affect circuit operation. So the remaining question is: What is the maximum discharge time your system can tolerate? This will set the maximum resistor value, and hence the discharge current.
ak