You have to select the model in the selection dialogue (immediately above your screenshot).
The 2pin connector (if you are using the standard KiCad libraries) is already in the library and is already correctly rotated.
If you want to adjust your own models, I strongly suggest that you investigate the Step Up work bench in FreeCad by @maui . Whether you use FreeCad or not for your design is not important but using FC for the alignment stage will save you a lot of work.