The show from the very beginning pitted the question of Faith vs Science, with Locke being a man of faith, and Jack being a man of science. Ultimately the show had to come down on one side and honestly I don't have a problem that it picked faith as science can't adequately explain everything either...at least by using faith offers latitude as it's a far more subjective concept then science which is bound by rules, theories and fact. That being said, Science did play a major role in the series and a lot of questions dealing with relativity, time and space were rooted in science.
Even if you consider the parralell universe theory... that's something which is possible and there are theories out there (super string theory, m-theory) which postulate that there could be thousands of multiverses and we could all be living different lives in them at the same time. Now, if you buy into that fantastical possibility which is offered to you by science then surely the idea of faith, god, good vs evil isn't too hard to swallow either.
As an atheist myself I think the show struck a good balance between investigating both the science and faith theories. Ultimately it picked faith, but at no point did I feel they were ramming the idea of god down my throat.
I also think they picked Faith because it's easy to understand on a personal level. If they had gone into hardcore physics to explain parallel universes and time travel you'd get just as many people saying that the writers were using hokey science to answer difficult questions. Bottom line is either choice would have had its critics.
That being said for me, even the science vs faith debate there are some similarities. Science points to there being equal and opposite forces at work in the universe. Matter and anti-matter, energy and dark energy, positron and electron. So the MIB and Jacob to me were just that, particles with diametrically opposite purposes which had to co-exist in the same world.
