The problem is that once the rust has gone past the filter (OP reported rust in second stage) then the iron oxide particles will act as an abrasive, causing premature wear of the plating on the inside of the piston cap. In my view a complete service is not a "waste" but a prudent step to take to help ensure the long-term performance of the gear.
I agree 100% I am a ScubaPro Tech as well as a longtime ScubaPro diver. If you brought this to me I would suggest a complete service on ALL stages. There are all sorts of places that the rust can get trapped and only a complete service and cleaning will ensure proper operation. Parts kits are not that expensive when you are talking about life support equipment.