So we're assuming that it's easy to classify something in the "proto-or-pseudo-science" box...all statements about which you aught to have low certainty go into that box.

Then, the way to distinguish between the two is the level of certainty that the person making the claim projects. If they are projecting high certainty for a claim for which they aught to have low certainty, then it's likely to be pseudo-science.

Creating an explanation with a conclusion already in mind (the Christianity example) is a subset of high certainty - since they started out certain of the conclusion before even examining the evidence.

If it's not pseudo-science:

1) The tone will be appropriately uncertain (and the person making the claim themselves points out the weaknesses)

2) There will be a sincere effort to reduce the uncertainty (suggesting further experiments, etc).