Capture with the Bishop or the Pawn .. Can someone help me understand?

I seem to struggle with what's the best way to capture, and in general terms, Pawn structures. In this game, after 7.Bxd4, I have two ways to recapture; exd4 or Bxd4. 

I made my choice based on what I understand as chess principles. 

Taking with the pawn, exd4 has the following drawbacks:

• I create doubled pawns on the d-file, therefore hurting my structure
• I give up control of the f4 square, allowing my opponent to eventually play f4, and control the e5 square.
• Potentially white can push the e pawn and gain tempo on my knight on f6.

So, I decided to take with the bishop. 

Stockfish doesn't like that. According to stockfish, the best way to capture is with the pawn. I am not challenging Stockfish obviously, but I don't understand why! 

Can someone help me understand?