Actually, you have two general options:
1) As I think you are suggesting, you can write some sort of intermediate software on the host system side which translates from the interface the existing software requires to the one the Arduino actually supports. In theory this should be a great solution; in practice some operating systems may make it difficult to install.
2) The ATMega16U2 USB interface microcontroller is reprogrammable, and the source code for the currently virtual com port firmware is available. Further, there are already source code examples out there for implementing different USB interface schemes in that chip (most may be aimed more at the Uno, but porting should be trivial)
The connection to the Arduino will be thus:
simulate this circuit – Schematic created using CircuitLab
You can use either an analog or a digital input pin on the Arduino for reading from the device. The specific values of the resistor and capacitor are not critical, so long as the resistor does not limit supply current below around 5 mA, which the datasheet specifies as the Absolute Maximum the component could ever need. This means resistor values of up to 1 kOhm will be fine.
The R and C in the datasheet application circuit example are there to eliminate any high frequency noise in the supply circuit. With 100 Ohms and 4.7 microFarad, this filter has a cutoff frequency of around 340 Hertz, so it will smooth out power supply noise over that frequency.
You could use 220 Ohms and 2.2 uF for a similar effect, filtering out any power supply noise above around 330 Hz. ... Or any such combination of R and C. No, don't leave out the capacitor, else the power filtering purpose is not fulfilled.
Neither the resistor nor the capacitor really have any relationship to the voltage the TSOP part is powered with - other than that the capacitor needs to be rated to operate at well above such supply voltage. Since the 2.2 or 4.7 uF capacitor is most likely to be electrolytic, ensure that the capacitor is rated for 10 Volts, and is connected with the correct polarity, i.e. negative pin connected to GND, positive to Vcc through the resistor.
Note that the datasheet states Supply Voltage (VS) of 4.5 to 5.5 V. While the TSOP series does operate at 3.3 Volts from personal experience, this is below the rated supply range, hence functionality is not guaranteed, and may occasionally fail.
Best Answer
No, it should not. The input for the GPIO pins are high impedance and you can tie them to VCC (3.3V Not 5V) or Gnd without issue. If you are trying to switch the input with a push button though, you need to switch between one state to the other. A pull up or pull down is used to set the default state, while being weak enough that it can be overridden when switching to the second state, and preventing a direct short.
Note that an input is a 3rd state, High-Z, not a direct connect to ground or vcc. This is fairly standard between different micro controllers.