Losing the skill as if they got twatted over the head with a branch and caught amnesia would be silly, I agree. That's not what's happening in-universe, though; instead of losing the skill, one who takes up being a cleric seems to take on certain restrictions from their god lest the god decide to start withholding spells, and one of those restrictions, however silly it might seem, is that the recipient cease to use certain weapons. The skill is still there, it's just that they can't use it without losing their powers (whether or not they all go at once or certain spells get withheld is a mushy area that would depend on the circumstances and the DM). It's not that Aragorn would forget who to use Anduril if he decided to spend some time to take on the duties of a priest, but rather that the god he serve would effectively be granting him power so long as he didn't use Anduril anymore.

Not really sure how that's supposed to work for Evil clerics, though; one would think that Bhaal wouldn't care if you shanked a dude with a dagger or caved his head in with a flail, so long as you killed him. Maybe that's a special benefit granted by clerics of Evil deities or something, I'd have to check. I kind of get the general sentiment with Good deities, as they generally tend to want their clerics to provide aid to others and not be inflicting more harm than is needed, but my Thor prayer points to the problem with that.

Pretty sure that's all rather moot in BG's context, though; so long as one of your classes can use a piece of equipment, you can use it regardless of class restriction, if Jaheira is any indication. Druids can't wear metal armor, yet her levels in Fighter let her rock a suit of full plate with no consequences. Just as well, because the game already has enough of a problem handling Paladins fall whey they are too naughty, and trying to handle the more nuanced consequences of denying certain spells based on how displeased a god is would require a program able to simulate the subjective thought process of a human DM.

This is the crux though, isn't it? Baldur's Gate is not P&P, and even in 3rd Ed the (stupid) rule has been dropped.