A macro containing the following line of code will align the separator to the right.
http://www.gmayor.com/installing_macro.htm
Code:
ActiveDocument.Footnotes.Separator.ParagraphFormat.Alignment = wdAlignParagraphRight
If you want the separator and notes re-aligned left then
Code:
Sub FootnotesLeft()
Dim oFn As Footnote
For Each oFn In ActiveDocument.Footnotes
oFn.Range.ParagraphFormat.Alignment = wdAlignParagraphLeft
Next oFn
ActiveDocument.Footnotes.Separator.ParagraphFormat.Alignment = wdAlignParagraphLeft
End Sub