A lot of people are assuming that Disney will do a soft reboot of the Alien series. Certainly, that makes sense if you look at how they've handled Star Wars.
However, there is also a strong possibility that Disney just shelves the entire film series for some time, possibly forever. While I am just speculating and do not claim to have inside information, if you examine Disney's business model, they are not in the business of small returns on investment.
Marvel, Lucasfilm, Pixar - they all invest millions and expect millions upon millions more in profit.
If the Disney deal goes through, they may took a look at Alien and decide that it doesn't fit within Disney's pre-established business model. Prometheus (a new take on the Alien series) made a decent return - but not the level Disney generally expects. Alien Covenant (a sort of throwback to the original) probably broke even/made a small profit. Also, not Disney's traditional standard for financial success. Disney is in the business of making a few movies - but all are expected to be heavy weights.
Unless they change business strategy, the Alien series may just not be what Disney is interested in economically.
People have to keep this one very important fact in mind - Disney intends to launch its own streaming service to compete with Netflix. That was likely one of the major reasons to acquire Fox - to get their vast library to place on this new streaming service.
They are not necessarily interested in re-launching all of Fox's storied franchises. There is of course a possibility that they could create an Alien TV show or even a lower budgeted movie made specifically for this new service (not theatrical release).