Seat height isn't much of an issue under real world conditions, and the are multiple options to lower a KLR.
KLR is a great bike on the highway, best of the 650 and under options especially for the price, and good enough off road to get you there. But I will say it doesn't handle actually trails, especially more technical ones, that well. So if you intend on riding it like a dirt bike (at all) you'd be better off modding a XRL, DR, DRZ or similar to be better on the highway then trying to take a KLR on the trails.
I'm actually thinking of dumping the KLR for a DRZ just to be able to ride the trails more. And I wouldn't be afraid to ride it across the county, with a few mods. I think the DRZ seems the most KLRish as far as build, aftermarket, maintenance, ect.