As much as I'd like A:I to have multiplayer, I just don't see it working.
Your first idea could work, but at any point at least two players wouldn't be bothered by the alien. You could add Joes, but I don't like them that much.
The second idea just wouldn't work, period. Joes would be instant winners - stronger than humans and invisible to aliens. On the other hand, people would be instant losers. Joes and aliens would be as smart as them, and that means they'd just check every possible hiding spot in the area where they spotted a human. It's not like they'd see a closet and just went by, like the AI does. Flamethrower would be useless (players already know it doesn't hurt the alien), noisemakers would be useless (it would just reveal that a human is nearby), and so on.
If somebody asked me for an idea for a multiplayer mode, I'd say: one player is in a safe spot and has a motion tracker - like Lambert in the movie - and he has to guide the second player, who doesn't have a motion tracker. It'd require a headset, but it'd be fun, I think.