Apartment Envoronment and thin walls. . . .
I use a .40 for carry and home defense and live in an apartment setting. I use the Federal Hydrashok 135 gr JHP and as I am in the building materials sales business have tried several loads to determine which one I will use. With the 2x6 wall studs required for a multi-level housing code and the use of fire retardant sheetrock (read 5/8" wetrock) with James Hardie siding on the outside and brick on the front along with the insulation packed into our building a 135 stops in the wall every time, no exceptions I've found so far from a 10'-15' range. WWB sails through without thinking about slowing down or so it seems. Older apartment homes will vary in construction and composition of wall area. Certainly if I were to shoot a the window, nothing to impede the round so far. I carry 155gr. JHP for CCW carry and have no fear of a substandard round. If I am confronted with a car being used as a weapon, the Mossberg comes out immediately. I have trained approximately 25 females to date with the .40 S&W and so far the weapon of choice for purchase has been the S&W M&P 40. Some have opted for the 9mm and some still for the Airweight style shrouded hammer revolver. This in preference to racking a slide. Your wife will be able to respond with a .40 due to adrenaline if in an actual situation, range time will be more cost effective and productive with the 9x19mm as stated earlier. In home defense there is no substitute for a 12ga. pump shotgun, rack one and listen. We even have a burglar alarm company locally that has a recorded sountrack of a 12 ga being racked when the alarm initializes. Cannot say whether it works or not, just sounds real and close. The best answer to any caliber/weapon is shot placement, not size. A head shot with a .22lr will be far more effective than grazing a leg with a .50 GI. Okay, I've rambled on for too long, thank you for your service from a former Marine, you as well Mike. Use what fits you and what you shoot the best with and practice, practice, practice, practice!!
Take a class...both of you
I don't own a handgun yet but I did just complete a 12 hour NRA course for pistols. If your wife is new to guns (like me) she has no business touching one until she completes a course. You could probably benefit as well. You'll learn a lot, shoot lots of guns of various calibers, see the drywall test (an amazing penetration demonstration) and walk out feeling a lot better about chosing the right gun and actually using it. Your military training will be more than sufficient but your wife should not be grabbing a handgun at 2:00 AM that she has only shot a few times with you.
Get up to speed on how to operate a handgun and also when to use it. The consequences of your decision will be lifelong and criminal and civil liability must be considered when you are reaching for your widow-maker. Don't shoot some two-bit criminal and end up supporting his family for the rest of your life. Save your shot for the violent criminal who you feel may take your life. Shooting at someone is a moral and financial risk as well as a risk to your personal freedom (or at least your ability to own a gun). Your life is worth defending, your stuff is not. Take a class buddy, you won't regret it.