The Deity Dillemma

We've been discussing a lot lately, (in class and on the blogs) about the aspect of philosophers who incorporate a deity to answer questions which seem to lead to no logical answer.  Obviously, for those who rigorously and logically analyze theories, this can be problematic.  My question is this; what should be done? I would like to think that some of the greatest philosophers that used God, or some kind of metaphysical mystery to convey an idea (Kant, or Aristotle's unmoved mover, etc) could not possibly conceive a better way in which to explain their theory.

Should theories that reach this point be thrown out?  Published for further criticism and advancement?  Or can their be a silver lining of truth in a theory that takes this form?

Kant on Perspective

As we discussed in class this week, Kant took the classic view of the world around us- namely, that we perceive what is around us- and posed the converse idea, that what we perceive is what the world is entirely.  
How does this seemingly subjective claim (everyone's mind is different) fit in with his objective theory of morality?