As in Paint.NET, by moving mouse while holding right mouse button.
March 1, 2015 Pinta 1.6 was released. See download page: http://pinta-project.com/releases
This feature was already in Pinta 1.5 as stated by Cameron bellow. To get this working you have to do:
1. Rectangle Select tool from Tools pad and select some area on canvas.
2. Move Selection tool from Tools pad and right mouse click on selection then move mouse up or down to have a rotated selection.
AdminCameron White (Admin, Pinta) commented
This was implemented recently (https://github.com/PintaProject/Pinta/commit/4a2b5ce49dca762ffbdc887287b7753d7239477d) and will be in Pinta 1.5