The Alien angle was something that was pretty much sticking around since the 90s, through multiple versions of the script. I think Spielberg and Ford weren't that keen on it but Lucas kind of stubbornly insisted on it. Earlier versions featured a more World War II setting, but as the project was constantly delayed and Ford aged they had to move things up to the 50s. One version of the script was even written by Frank Darabont, and it included the fridge scene.
Lucas also had the idea for Indiana Jones in a haunted house or castle, which I suppose could've worked. Spielberg worked (Although opinions differ on how much, although it's his story) on one of the more popular old school haunted house movies (Poltergeist) and it can definetly been argued that Indy's had dealings with spiritual beings anyway. Although I'm not sure how they'd work the archaeological/globe trotting aspect of things to it, although TOD was largely confined to one major location compared to the other films.