It wouldn't be a bad idea for the next season maybe but the impact on the team on the medium range will be bad imo. Bayern is planning for the long term, on how they could maintain their dominance in Bundesliga and try to catch CL title. This requires a stable and relatively young team with some productive and experienced players like Lewandowski. Having CR7 will make the team rely on him and once he is out after a year or two there will have to figure out a new plan. Real Madrid and Juve suffered from that although the impact on Real was bigger but they managed to pass it thanks to Benzema and V-Junior mainly.
Anyway, the announcement of Bayern to not accept him in the team is good and reassuring. I respect their courage to say that publicly.