What kind of air is the organ currently getting? Ideally the blower should have a well-filtered intake (like actual filters, not a piece of cheesecloth), to keep the insides of the chests squeaky-clean.

I have never heard of magnets being “gummed up” by incense. Unless the intake to the blower is right by the altar, you shouldn’t be looking at any significant risk; or put differently, there is nothing particular about incensing vs any other thing that happens in churches (not the least of which is significant temperature and humidity swings) and it is an occupational hazard, of sorts. Organs have dealt with it for centuries. Every organ needs re-leathering every 30-60 years, even without significant incense exposure. If you are having regular and perpetual issues with your valves, I highly suspect that something other than incense is at play (poor craftsmanship, poor design, sub par components, or insufficient preventative maintenance, etc.).