Supposedly you can "step down" the pipe before the muffler. Since exhaust decreases in volume (hope I've got the terminology right) the further back you get, the less space you need to provide adequate flow. Actually you can help by keeping velocity up.
The one exception is of course any restrictions. Which a muffler is. Theory says that a larger than pipe diameter muffler of good design is of less restriction than if it were pipe diameter. So small pipe, big muffler in/out, isn't a bad thing.
But I'm not sure that would change the muffler resonance. I'd expect it would based on changing the exhaust pulses, but I'd be leery of shelling out the bucks to find out if a 5' section of 2.5" pipe before the muffler solves the problem.
I've always wanted to experiment with it, but unless you've got some spare parts or cash laying around, it's pretty difficult, especially if it's not a straight run of pipe you are replacing.