The main difference between men's and women's frames is the relationship between stand-over height (or seat tube length) and effective top tube length (the distance between the top of the seat tube and the top of the head tube). Women typically have longer legs and arms and a shorter torso for their height than men do; therefore, women's frames have a shorter effective top tube length for the same seat tube length compared to men's frames. Not all men fit best on a men's frame, and not all women fit best on a woman's frame. Two of my adult daughters ride a men's frame, and my other daughter and my wife ride a women's frame.
An experienced bicycle fitter should be able to help you determine which is the best fit for you based on your body proportions, flexibility, physical conditioning, and cycling goals. When I bought my road bike, I was coming from a hybrid (Specialized Crossroads). One of the fitters at my LBS spend about four hours working with me to determine the best bike and the best setup of that bike before I bought. Going in, I was considering the Specalized Sequoia, Roubaix, Allez, and Tarmac; the Trek Pilot, 5000, and Madone; and the Felt f5c.
At the time, I was 54 years old, 200 pounds, 6'0", short arms (33" sleeve) and legs (30" inseam) and limited flexibility due to spinal stenosis. My goals were to ride long distances (75 to 100 miles) at a moderate pace. I have no intention of racing, but I did want to be comfortable over long distances.
With the help of the fitter, I quickly dropped the Allez, Tarmac, Pilot, 5000, Madone, and Felt from my list (the same shop carries all of these bikes, BTW, so there was no bias on the part of the fitter). After spending some time on the trainer making adjustments to the remaining bikes on my list and after a few test rides on the road of about 3 to 5 miles each on the Pilot and Roubaix, I decided on the Specalized Roubaix Elite. Three weeks later, I road that bike 75 miles per day on two consecutive days without any discomfort. I averaged 17 mph on the first day and 15.2 mph on the second day, which was well within my expectations.
As far as the fit is concerned, what you need to look for is the distribution of your weight among your feet, hands, and butt; the position of your knees in relationship to the pedal axis; the extension of your leg when the pedal is in the downward most position; whether your sit bones are positioned on the proper part of the saddle; and the position of your back when your hands are on the hoods. Again, an experienced fitter will be able to help you sort this out. In my case, he had to replace the stock stem with a shorter one so that my reach was comfortable.
I do not agree with your statement "We are used to riding mountain bikes so any road bike would feel uncomfortable". A properly fit road bike will feel different than a mountain bike, but a road bike should not be uncomfortable. If it is uncomfortable, and if there is no one in the store that is willing (or has the knowledge) to take the time to find a bike that fits you properly, then find another LBS.