One thing you should remember is even though the S50 is a fairly light bike it is an 800cc bike afterall. Are you sure you want to give her that much power for a first street bike?
The S40 is a 650cc but it is also a light bike and fairly nimble.
These are some seat heights and weights:
Honda Shadow VLX 600cc – 25.6 inches 496 lbs
Honda Rebel 250cc – 26.6 inches @ 329 lbs
Yamaha Virago 250cc – 27 inches @ 302 lbs
Vulcan 500cc – 28.1 inches @ 439 lbs
Suzuki S40 (650cc) – 27.6 inches @ 381 lbs
Suzuki S50 (800cc) – 27.6 inches @ 478 lbs
It is not simply just seat height, but the engine CC’s, and the weight of the bike as well. All these will be factors on fast and well she will learn. Though not impossible to learn on bigger bikes, it is definitely faster and more enjoyable to learn on a smaller displacement bike.
I know a lot of people who started on a 250 and still riding the same bike. It all boils down to what you will use it for and from the sounds of it just crusing from town to town. My first bike was a Rebel and she did fine on freeway doing 70-80mph. I just had to get a bigger bike because I literall commute on mine almost 700 miles a week now and Houston traffic is not forgiving at all.
Just think back when you first riding. It’s not simply if you can fit the bike, its more if the bike can fit your needs and skills. An in my opnion an 800cc is way too much to start on. The MSF course will probably be the decision maker; if she finds the slow tight cornering to be difficult on those 125/250cc bikes then think about how much harder it will be on something larger.
But ultimately its going to be you and your wife’s choice. Just be safe and smart about it.