In the piece, penned by Maureen Orth, it was alleged that Cruise prepared Iranian actress Nazanin Boniadi to be his wife shortly before he went public with Katie Holmes.
Former scientologist and director Paul Haggis later backed up the claims, although they were denied by Cruise's reps and the Church of Scientology.
Alley, who also practises scientology, has now defended Cruise in an interview with Entertainment Tonight.
"I think whenever you have articles written that are third and fourth parties' opinions, it's like the game Gossip and you don't get the truth," she said. "I think a magazine of that calibre should have interviewed him and then they would get the truth."
She added: "I don't like it when any magazines have 'she said, he said, they said' - then it becomes a gossip magazine."
Alley also defended scientology in general, saying that it is "so normal" to her.
"I think that probably all religions sound bizarre to people who are not practitioners of them, and that's the only thing I can think of," she said. "We're pretty outspoken about different things."
She added: "Probably 90% of the crazy stuff I hear isn't true."
Orth later told Entertainment Tonight that she requested an interview with Cruise but was declined. Cruise's lawyer has said that the star "probably won't sue" over the piece.
Watch Kirstie Alley speaking with Entertainment Tonight below: