If the bike came like that from the factory I wouldn't worry about it since OEM's are usually conservative about that sort of thing. I don't know how a FD would know the difference between a 48 or 52T chainring (they're very simple devices.) With FD's I thought the only consideration was the the number of teeth it needs to go from the highest to lowest chainring on the crank.

As far making the front shifter into a double that is very easy to do. They would just mechanically lock out the third position using the limiter screw on the derailleur. This is exactly how they do on the new Trek 7.5FX (Deore front shifter with a compact double crank.) I did the same thing on my last road bike when I converted it from a triple to a double crank.