So long as they adhered to whatever safety protocols governed the containment of virulent organisms, I see no reason why Bishop would have disobeyed Burke's orders. My belief is that Ripley knew this too, which is why she had to resort to threats of tattling to the ICC about his specimens.
It's also my belief that bringing dangerous specimens back to Earth wasn't illegal, but smuggling them was. Burke may have been afraid, like before, that a bureaucratic quagmire would have jeopardized the reward he was expecting for quietly delivering the aliens to the company labs.