One trick I learned last year to fix defenses was to add 1 point for 3 and outs, and possibly 2 for 4th down stops (which may as well be a turnover). They're things I always figured defenses should be rewarded for anyway, and the 3 and outs happen often enough to bring defense points up by themselves.
By doubling the points earned from points allowed, it really only affects the high end of defense scores without touching the low end.
Of course, I don't mean to tell you how to set this all up. I'll be fine with adapting to any setup, so they're merely suggestions.