Just eliminate it entirely as a really poor design decision in the first place. It’s totally not necessary.
The effects of the template should be role-played. So the character should have to struggle with primal urges and the like, and the player should try to make this interesting and part of his character’s story. But his alignment should not arbitrarily just change. The alignment change should be treated as a thing that happens to the weak-willed, perhaps, or to commoners unprepared for the magical assault on their bodies, minds, and souls (as adventurers, even low-level ones, might be). It might be a thing that could happen to a player, if he indulged those urges. But not automatic.
I don’t particularly like the idea of Will saves vs. compulsion to enact said urges. A good roleplayer shouldn’t need to be forced, and ultimately the effects of a few bad rolls in a row could be very problematic for keeping the player’s character as the character he wants to play. This kind of mechanic could be done well, but ultimately I’d rather just make it a plot-device that the player can play with. And if the player isn’t interested in doing so, then I really don’t think making him roll Will saves is a good idea: it is a game, after all. Forcing the player to “play” a game he doesn’t enjoy doesn’t make much sense, and strikes me as rude.
Alignment Usually Isn't Hard To Determine
Alignment often isn't that hard to figure out anyway. Spells that can detect it are readily available, some classes (like Paladins) can detect evil as much as they want, and in certain cases you can discern it from their actions (a Cleric casting a Good spell can't be evil, because a Good type spell can't be cast by Evil Clerics).
It's possible to take steps to conceal it, but in my experience not many people do that.
So I don't think the real risk here is that you're going to make alignment too easy to determine.
Overemphasizing Alignment
To me, the biggest concern is that by having the world reflect alignment so readily, you're making it more important. Being Good is so important in your world that all magic is affected by it, even when the spell is thematically neutral and doesn't do anything that relates to alignment.
You've elevated alignment to be a more prominent thing. Considering how rigid the alignment system can be and the problems it can cause with player behavior, that's not something I would want to do.
Consider what that means? Normally if I see someone cast a Fireball to take out some creatures, I'd just determine what to think about that based on what I saw, and if I cared about those creatures or not. But now I'm seeing an Evil Fireball. If I'm a Good character, do I have to do something about the evil spellcaster? What if they're on my side? What if the people they're attacking are also evil, but those people are using weapons so I can't tell?
The alignment is so in my face that it distracts from trying to figure out the motivations of the people involved, because literally the first thing you've told me is "that Wizard is evil."
Best Answer
Not as written, but if you decide Lareth has a Helm of Opposite Alignment, he could accomplish it that way. This would require tricking or incapacitating the cleric, such as with a Hold Person spell. On the other hand, that's a pretty rare item to use up on a 1st level cleric, when a villain could generally achieve more with a higher level character.