Staying at a motel with a lobby rather than rooms that open to the outside might be safer. There are no guarantees. Ever.
Driving through at 11:30 might be tough to find. My advice would have been stop in Moriarty, or drive on to the big casino/hotel 30 min west.
Much safer than Albuquerque.
When you're driving cross-country and you have a vehicle filled with stuff you need, it's a lot easier to get a motel room where you can back your car into a spot in front of your door. I've done this many times. Always keep my .45 close by as well.