Then you are second guessing the playcalling decision to run on 2nd down, which is a different question from the penalty decision to take the yards.

Take the penalty, it's first down, you have 3 downs to get 10 yards = you need to get 3.3 yards per play, from the 21
Take the 2nd and 3, you have 2 plays to get 3 yards = you need 1.5 yards per play and you're out to the 23. Better field position, lower yards to go, higher probability you'll get it in two tries.

It has nothing to do with having a good running game or not. It has nothing to do with your emotions about the Saints, wanting them to pass more or your opinion on not wanting them to run. It's about probability, which is easier/harder or more likely to be achieved -- 3 downs to get 10 or 2 downs to get 3. You're saying in that situation you'll "take" the 1st and 10, and that's fine, that's your decision, you're the coach -- but you are taking the harder path to achieve success, with a more difficult probability to get it.

Plus, when Brees is that close to our own goal line, it also makes sense to take the yards, to go forward, and keep going and get further outside the 20. Because that is the area of the field where fumbles and turnovers going the other direction are especially dangerous. Brees just had one the week before and he had thrown a pick 6 last year against Carolina in almost the same exact field position.