The best solution for these low voltage drives would be a regulated (switched mode) power supply combined with a clamp circuit. That way you could safely operate a 48V drive at around 45V or so, to exploit the higher speed capability to the full. I haven't seen a clamp circuit available or in use (haven't been looking, mind) - is there something readily available on the market?

It tends to be periods of rapid deceleration that result in overvoltage due to regeneration of the kinetic energy back into the DC bus. One simpler option might be to limit the deceleration setting (or acceleration if not controlled independently). That way you could run fast rapids as long as your e-stop didn't try to force a quicker stop.