And I would love to see the religious bend-over-backwards explanations as to how a soul binds to a machine instead of the brain.
Well, Lxanna Troi seems to think that thought and life are interconnected. The Travelers believe that thought, space, and reality are the same. If you want to treat the hokey New Age spirituality seriously versus Orthodox religion - basically, "A soul exists because a person thinks for itself." Whether said person is metal, steel, plastic, crystal, or an ugly bag of mostly water doesn't matter.
Of course, taking this philosophy to its natural conclusion means that the universe of Star Trek is essentially the Matrix.
(I actually use Star Trek in my religious studies group as it has some nice ideas for examining the nature of theology)