Welcome deetz!
As a shorter guy (5'7" if I eat my Wheaties) I can definitely sympathize with your wife's challenges. Good that you're looking to do seat mods instead of lowering the bike... that's the best path.
Consider picking up a second seat on eBay to shave. The process is not reversible and will likely affect your ability to sell the bike.
I can tell you first-hand that while it seems really scary to have a too-tall bike at first, it does get better with experience.
There are a few other things she can do to help that require no mods to the bike. If she's a rank beginner, chances are she really wants to get both feet firmly on the ground at the same time... including getting a heel down. Important for confidence while learning, but not truly necessary.
She might try learning to shift her butt to one side a bit so that she can get one foot, or at least the ball of the foot, firmly down even if the other is just on tip-toe. This takes some confidence that the bike isn't going to just fall over, but it certainly does work. My track bike is an R6 (seat height a few inches higher than my inseam) and I'm on tippy-toes when sitting square on the seat. Just having one toe down at a time and shifting over when I need a foot down is how I manage the bike. I will note that I did shave the seat but it's still "too tall for comfort" as they say. If I had to go with the stock height I could.
Another thing is to get as tight up against the tank as possible when getting a foot down. This allows a more upright posture, which rotates the pelvis and in effect allows the legs to be "longer"
Here are some pics of Dani Pedrosa. He's all of 5'4", so short his feet actually dangle a couple of inches off the ground when he's sitting square in the saddle. Check out that pic of him standing next to the bike!
While he does have mechanics there to hold his MotoGP bike for him in the pits, he still has to hold it up on the grid. He does it by shifting to one side.
