I vaguely remember coming across German government websites earlier in the pandemic that advised travelers with complicated travel situations to contact the Bundespolizei at the arrival airport via email. For Frankfurt that would be [email protected]

Perhaps if the OP reached out to them with essentially the same information as provided here (maybe including the flight details for the connecting flight), the Bundespolizei would reply via email confirming that they would let them into the country for transit purposes, and perhaps having that email might increase the chances that the airline will accept them.