I looked through the theme files and the other setting files and it seems like the size of the cursor is hard coded. You could try to just edit the simple crosshair sprite in the theme to make it less intrusive. You can make it both smaller and semi-transparent which might make it somewhat of an alternative at least.
You can try this example theme edit I made: Dropbox - aseprite-theme-alt.aseprite-extension - Simplify your life
Should be able to just double click the file to have aseprite install the theme, then change to the theme in preferences.