Reworking on your code I second the suggestions @Computable posted in the comments section. I would leave the else-block in and also delay the re-read in the if-block to avoid polling the input too often. Try and refactor your code to this:

void setup() {
 pinMode(9, OUTPUT);
 pinMode(2, INPUT);
 digitalWrite(9, false);
}

void loop() {
  if(digitalRead(2)) {
    digitalWrite(9, true);  // activate pump
    delay(3000);            // let the pump run for 3s
    digitalWrite(9, false); // deactivate pump
    while(digitalRead(2)) { // wait until hand is no longer close to IR sensor
      delay(.5 * 1000);
    }
  }
  else {  
    digitalWrite(9, false); // deactivate pump
    delay(.5 * 1000);       // This avoids looping too often (re-read IR sensor only every 0.5 seconds)
  }
}

Please share the results!