I found a solution eventually to have the pin cites on the right without having my text in a 2 column table.

1. Edit the normal style to allow 2" of right margin.
2. Use a text box to indicate the cites.
3. Make sure that the anchor of the text box is placed at the paragraph which the cite is referring to. In this way, the text box will move accordingly if the paragraph is shifted.

This solution's a little tedious, but it beats using tables to me.