Well I can fully sympathise with that! (Witness my rantings elsewhere on this board over my experiences with a witless TA.) But, assuming you want the triangular routing and are forced to deal with an in-house TA, can't you just say to her: "Please book me in L class on the following itinerary LHR-NRT-xHKG-xJNB-CPT-LHR using only JL, CX and BA. The fare basis is LONEWC3 and the fare is GBP1179 (1289 in high season) before taxes. The BA/CX/JL reservations desk will assist you if you are having problems."

The last statement is more a hope than a promise (at least for CX in JNB) but at least it should get her to start going in the right direction.