I have this problem on my commute. I use the shared bus cycle lane for part of it, and the road is set up so there two traffic lights, one for the bus lane, one for the single carriageway road. There is no 'junction' per se. Its designed so that the second a bus pulls up, the lights for the traffic go red and let the bus through. The bus lane then ends about 20 metres further down and merges with the main traffic lane. The 'cycle lane' actually continues, though its hard to call a faded line painted about 50cm from the edge of parked cars a cycle lane.
I have found from experience that if I stop in the bus lane, the lights won't change for me. Ever. Unless a bus comes up, which is about twice an hour (this ain't London!). I can therefore either pull into the traffic lane, and share their lane with them whilst going through the pinch point caused by the traffic lights and the keep right arrow, or I can go through the light on red in the bus lane, withthe traffic still moving, and by keeping to the left simply carry on and 'naturally, rejoin.
This is the one set up where even I RLJ, and I can't see an issue with it. Even the most anal policeman would surely agree!