If I buy a paper zone 1&2 travel card then surely I'm going to have unresolved journey problems
when I touch-in with the Oyster in a zone 3 station but use the paper travel card to exit a zone
1 station at the end of the same journey.

Is there a sensible solution to my problem?

You should do as you suggest and buy the paper ticket. If you only touch in
or out in a zone where the season travelcard on your Oyster Card is valid
but not at the other end of your journey, it is assumed that the other
"untouched" end of your journey was at National Rail station where your
travelcard was valid (and there were no barriers/validators).

Unresolved journeys only ever occur when you only touch in or out at a one
end of your journey and you do not have a valid season travelcard for the zone
that station is in.