The database columns which store points are integers, so cannot contain decimal numbers. So I would recommend running Q2A will all points multiplied by a 1000, and then dividing by 1000 only at the presentation stage, i.e. when the points are converted to HTML for display.
You can search the source code for number_format and then wherever that is used to format points, make the change. For example in qa-page-users.php, change:
qa_html(number_format($user['points']))
... to ...
qa_html(number_format($user['points']/1000, 3))