There is a dislike of God-of-the-gaps arguments in the theological and philosophical community. A God-of-the-gaps argument is an argument for a theistic explanation of a feature that does not have a scientific explanation but where, as far as we can tell, a scientific explanation would in principle be possible.
But suppose that there is currently no good scientific explanation of a puzzling natural feature F of the universe, although we can give a good theistic explanation of F. This is likely to be evidence for theism. After all, if F is puzzling, then our best theories presumably do not predict it. Thus, given what we know, F is very unlikely on the naturalistic hypothesis. But if we can give a good theistic explanation, F is not going to be very unlikely on the theistic hypothesis. A good theistic explanation of F in this context will have to give reasons that God would have for actualizing F, and will have to give an argument for why God is not unlikely to act on these reasons, given the relevant background assumptions. This is not an impossible task--e.g., God would have strong reasons for creating persons, because the existence of persons has great worth, and a perfectly good being would be not very unlikely to act on such strong reasons.
Now, if F is evidence for theism, then surely a rational person cannot fail to consider F just because the evidence falls is of the "God-of-the-gaps" type. What matters evidentially is not whether the evidence is of the "God-of-the-gaps" type, but how much confirmation that evidence gives to the existence of God.
It may, of course, be that some evidence needs to be excluded for certain purposes on non-evidential grounds. Thus, a priest needs to ensure that his public interaction with a penitent is not affected by what he learned about the penitent in the confessional, lest inferences about what the penitent confessed be made from the priest's behavior, and it may be that the best means to that end is for the priest to exclude information about particular persons gained in the confessional from his general stock of information for making inferences. But it seems unlikely that the class of "God-of-the-gaps" evidence is at all analogous to cases like these.