Hello,
I assume the transistor in the H-bridge is NPN, and you require to source current from the pin to turn the transistor on. As you have found, PTA4 may not be the most appropriate allocation for this purpose. The turn-on current through the 1k resistor will exceed the internal pullup current, and it also means that the transistor must initially conduct during POR, which may potentially also not be very satisfactory.
I think the use of a capacitor at the pin is problematic. You would likely need a value significantly greater than 1uF to hold up the input for the required amount of time. The presence of the capacitor will have other undesirable side effects. Since the capacitor would need to charge or discharge whenever the output changed state, this would slow the switching operation, and place additional stress on the output pin. You would also need to consider how the capacitor is to be discharged when power is removed - there is some potential for causing damage to the MCU.
If it is not possible to re-assign the I/O pins, I think you would need an additional buffer device between PTA4 and the NPN transistor. This might consist of a P-channel MOSFET, or a PNP bipolar transistor (plus base resistor). This would also ensure that the NPN transistor remained off during POR.
Regards,
Mac