I have done that with other processors, and it has worked well. But I only do hobby stuff, not production design. In the end, you might want to just try it and see what happens. If the internal pullup is 40K, and the DC gain of the transistor is at least 90, then switching 6mA should be no problem. And if the GPIO pins are floating on powerup, I don't think the transistors will turn on, even momentarily. That leads to the question of how you would turn the transistors off. In theory, you could just disable the pullup so the port is floating. Without base current, the transistor should turn off. But in a very noisy environment, you might want to change the port to output, low. Just be careful to change it back to input first to turn the transistor back on. You don't want it to ever be output, high.
Well I'll defer to the judgement of the EEs here, but my suspicion is it would work just fine.