From the UEFA website:
http://www.uefa.com/european-qualifi...d=2506867.html
With matches against the bottom side in the six-team groups discounted, the runners-up are ranked by the following criteria, in this order, as per FIFA competition regulations, article 20 paragraph 6, criteria a), b), c), then h) and i):
1 Highest number of points
2 Best goal difference
3 Highest number of goals scored
4 Fair play points (first yellow card -1pts; second yellow card/indirect red card -3pts; direct red card -4pts; yellow card, direct red card -5pts)
5 Drawing of lots
This suggests to me that goal difference earned against the bottom side is discounted, like points won, hence us having a GD of +2 on the table of 2nd placed teams.