Hrm.... Depends on what type of handling you're looking for.
For what little it's worth, I've never really noticed the whole "high BB" thing when switching between my cross and road bikes. I'm a bit skeptical that it really makes that much of a difference.
By the way, Tubus makes several racks that are both further back and lower than standard racks. Topeak also makes one or two that are lower.
Anyway.... Generally speaking, touring bikes are more stable than most cross bikes, which are slightly more stable than racing-style cross bikes, which are slightly more stable than "endurance" road bikes, which are more stable than standard road bikes, which are more stable than aggressive / racing road bikes.
Disc brakes are (
afaik) rather rare on road bikes, a little more common on touring, and much more on cross bikes. IIRC the UCI is now allowing cross racers to use discs in competition, so I'd expect a lot more cross bikes with disc brakes in the next year or so.
The only mass production touring bikes I know of with discs are the Jamis Aurora Elite (which is basically a cross bike) and the Salsa Fargo (kind of a mountain-touring bike).
So, I'd start by trying a Tubus rack; if that doesn't work, then start looking into new frames or a new bike.