Thompson is pro free trade, ain't no doubt about that, with the exception of Duncan and Ron Paul (whose opposition is more along the lines of how it is done, over it in and of itself), they all are.
Now as for wanting a NAU, considering Thompson is in favor of border security first, opposed to amnesty (see national review), it would be bizarre to see him supporting something like the NAU, and about as likely as Tom Tancredo.
And NAFTA, like it or hate it, is a done deal, signed and law.
Hell, did we give up sovereignty by creating NORAD with the Canadians? Seems that something like NORAD is a lot more testing to one’s sovereignty than trade agreements.
This isn't 1900, the economy is global, whether we like it or not... and capitalizing on the global market does not automatically effect your sovereignty.. Not playing on that field, however, does risk your existence.