Pump in bursts, allowing enough settling time between bursts for the pressure sensor to stabilise to an accurate value.
You can measure the rate of change between bursts to get an ideas of how long the pump must run to achieve a particular pressure, then if it's a long way off the target, use a long pump run to get to eg. 90% of the target before stopping and testing again.
That's pretty much how automatic car tyre inflation machines work, if you have ever use one of those - they have the exact same problem that the pressure sensor is near the high pressure air feed, with a long hose between that and the tyre.