The only problem I see is that a human alien player isn't going to retreat if the weapons can't harm it.
You'd have to be very clever with your level design to negate a human players tenacity.
If a flamethrower only holds the Alien in place like it does in Isolation for instance, you know that human player isn't going to flee, he's going to wait for the other player to run out of fuel and simply bumrush when it is over.
You'd have to have levels set up in a way where a human player could use the flamethrower, hold the alien, and then close a door, and then design the level where the Alien had to backtrack through the air ducts or subflooring to have his next shot at the human.
Any other way and you have a broke ass game where the human playing the Alien just mauls everyone to death because they can't stop it otherwise.
I'd have the Alien killable personally, but maybe have the Alien having the respawn ability after capturing other players for host.