Alignment calculation worker threads are not destroyed before AlignViewport references nulled

Long running conservation calculations can throw exceptions after the alignment window is closed that can affect behaviour (particularly tests). These are due to the threads running on after the alignment viewport and associated classes have been nulled.

Ideally, workers should be halted before references are nulled when the viewport is closed. Alternately, worker threads need to bail if it finds references it holds to alignPanels, viewports and its calcManager have been nulled by another thread.