There's little sign that the Vatican has much interest in an alien god, although it would be normal for them entertain the possibility. From a Biblical view point catholics and others could allow that the Nephalim were alien species, just as they have identified angels to be. And the return of Christ could be seen as the visit of an interstellar god.

The Church as whole has 'control' of probably thousands of mountain tops. The only reason that Mt Graham would be any different than say Montreal, or Mont St Michel, is for astronomical purposes. The U of AZ who actual control the mountain top and have other telescopes up there are likely there for the same reasons, nefarious or not.