This is an important distinction that doesn't always come across from ID folk. Christianity has a fine and proud history of humanism so this failure to make a distinction between the practice and philosophy of humanism amounted to throwing the baby out with the bath water. Lets not do this with naturalism. When it is used as a delimiter, I cry foul. Empiricism as a delimiter of science is appropraite and fair.
Empirical evidence is the primary way that belief is justified in the arena of science.
However, in the metaphysical arena empirical justification of belief is neither required nor often feasible. This is a failure of recognition rather than an errant philosophy of science. Let's let the data lead us where it will. One can make hypotheses from analogies, but then one must look for independent evidence that the analogous situation actually behaves like the prototype situation. The alternatives Jim presents above are not necessarily mutually exclusive.