When you lower the bike it will change the handling in some way.
For the front you can raise the forks in the triple tree about 10-15mm. This will decrease the trail of the front will and make the bike more twitchy, but turn in faster. Need to invest in a good steering damper like a Ohlins or Scotts if you do this. Either of the dampers are very good quality IMHO.
In the rear you can lower the bike with an adjustable dog bone. Then you could lower the bike about 3" in the rear. This part is abour $130 dollars or so. Lowering the rear will give the bike way less ground clearence and make turning much more difficult. This part was designed for drag racers.
Then you could get the Corbin seat for the R6. Their website says it will lower the hieght by about 1" or so. I think this is the best bet.
Have you looked at the SV 650 for her? At the last track day there was a female instructor on one. She was way faster than I on the R6, so I know they are not slow! Just a thought.
The only reason you would have problems with steering in turns after lowering would be because you did not drop BOTH the rear AND FRONT. Lowering your bike correctly will make everything gravvy. As for tankslappers, I take my bike up to 155 regularly and there is no sign of it. The older models had that problem and a dampener was recommended, but the '03 is a whole new design. It only needs a decent rider to be a great bike.
Scraping the bottom of your bike (where no one can see it) because you lowered it to be able to reach the ground and have confidence stopping on inclines is better than falling over and getting your clutch or brake lever snapped off, and scraping the sides where EVERYONE can see. As long as you don't weigh a few hundred pounds and you bounce on your bike, you should be able to make it over most speedbumps. I usually go through a low spot, or around in the raingutter, but it isn't really a problem.
The only scrapes visible on my bike are on the lower sides of my fairings, and the lower edge of my exhaust from getting over so far in turns. They go well with the nonexistant chickenstrips on my tires.