Well. To begin with, if you and your wife are certain of your size(s), and you can make adjustments to swap out stems and such, you will have no problems with the Motobecanes. As long as you want to be responsible for fitting and adjusting for comfort, especially for your wife, then there are no compelling reasons to discourage you from going the Bikes Direct route.
Your bike shop person raised two objections: obsolete/older geometry and assembly/adjustment. Okay.
Did he offer what he would recommend for you instead? And at this price point? Did he offer to have you test ride his competitive offer?
I ask because you and she might benefit from slowing down a bit and trying out some different bikes with alternative geometries: endurance versus race, which generally affects how high the handlebars are placed and somewhat the riding characteristics of the frame. Anyway, my recommendation would be to not rush into buying a Bikes Direct bike until you are convinced that the resulting ride will be what you really want/need.
That's a heck of a lot of bike for your first true road bike, by the way. You should go with a lesser group and both be quite satisfied for years. Just saying...