The Company doesn't need to know shit.
In fact, i've always said I thought the far more chillng idea is that everything that happens in Alien is due to an AUTOMATED system. Ash reassigned to the ship, the Nostromo sent to check things out... All part of programming that was already in place, and there's not really anyONE on the other side of it. Oh sure, the people in bioweapons division would be all over that shit, but they didn't actually conspire to do it.
That's actually based on nothing but my own imagination, but I still like it. In reality the intention was always for the situation to be the acts of a few looking out for their own bank accounts. Seeing dollar signs. Cutthroat corporate behavior. It was NEVER supposed to be that WY was somehow a big bad evil. Negligent, bloated, and unaware of what was going on more than likely. I doubt the execs at the top would want to jeopardize all of their interests on such a "risky venture." Of course, if it had been successfully carried out, they would embrace it, try to make it their own, but that's the corporate machine for you.