To answer your question whether you should have set a bigger aperture.
First, note that the question can be rephrased as 'is this an appropriate situation to override Nikon's matrix metering?'
Looking at the shot, the answer I would give is 'No'. I suspect that it is a bit dark due to the printing process rather than incorrect exposure (however, I suspect the print will look just fine). Matrix metering doesn't fail in this kind of simple situation.
Composition wise, pretty nice. At first I thought 'crop' to frame her with flowers, but this way is also good. Pity about the little post/stake/stump on the lower left
oh.. din notice that little pipe there.... agreed that it caused some distraction to the pic.. and on recalling back, i think i left the polariser on cos i was shooting the clouds prior to shooting the gal.....