If stains on walls / soot deposits only appear in the spots you’ve described, it sounds like you have a house insulation problem. Even without burning candles, those areas would most likely become darker just from dust particles sticking to colder surfaces.
Of course, soot from the burning candle flame accelerates “darkening” / appearance of ghost marks process. By using the humidifier, colder spots on walls will have slightly higher moisture level and soot / dust will more likely stick to that spot.
Air purifying equipment should help to reduce amount of soot particles in the air, but not all of the purifiers are alike, so do some research before you invest several hundreds of $$$ in it. As for the clean-up process, depending on contamination, complete stain removal might not be possible.
This 3 step method sounds promising – Soot sponge. In addition, check this article about candles, your wife may never use them again – Candle Soot Damage.