Welcome! 
Well, I never played KQ2 and I'm wondering if we know why Valanice was locked away in the tower in the first place?
Yes, we will. 
Aha! Since you answered in the future tense, I take it that we will learn something
new about why Valanice was locked in the tower.
The question now is whether you accept the backstory in the KQ Companion, particularly the explanation as to why she was locked in the tower. If you accept that explanation, yet we will learn something new regarding why she was locked in the tower, then either there was a second reason, beyond her beauty and goodness, or there will be an elaboration of the first reason, such as what she did to be so good. Are you at liberty to tell us whether you accept the KQ Companion's explanation and backstory, or is that question sufferable?
If her goodness was one of the reasons that she was locked in the tower, then that destroys my theory that her secret is something bad that she did. In that case, her secret might be something that she did while she was in the tower. However, since she had no freedom to do much of anything while in the tower, her confinement being much like solitary confinement in prison, then that doesn't seem to be a likely explanation.
On the other hand, if she was locked in the tower for something bad that she did, then that could be her secret. However, since Hagatha is a villain, it doesn't seem likely that she would have locked Valanice in the tower for doing something bad.
So, we have the following facts:
- Valanice has a deep, dark secret.
- Deep, dark secrets are of something bad.
- A bad person imprisoned her.
- If a bad person imprisons someone else, it's unlikely to be for something bad that that person did.
The only reasonable conclusion we can draw from these facts is that Valanice is neither completely good nor completely bad. She was probably a basically good person who was compromised in some way. That makes sense because, for example, the mafia doesn't take out contracts on good people who mind their own business, but on people who have crossed them in some way. So that's probably what happened to Valanice.