Defend the 3 if you can do it without the trade off of giving up the rim.
Defend against penetration first, always! If opponent is hot from 3, it's a tough game. Must keep opponents' 2pt FG% down to have a great team.
Here is one of Pomeroy's pieces on the subject, which BTW, shows BYU as among the best at defending the 3 under Coach Rose. One key point is if teams defend the paint, opponents don't do that great on 3s, perhaps due to taking higher risk shots from the arc.
Paradox: best defense against the 3 is to defend the rim!
http://kenpom.com/blog/index.php/weblog/entry/one_last_post_on_3p_defense