From what I understand, anyone could have destroyed the Time Devourer by fighting it in the Darkness Beyond Time. Hypothetically, Belthasar could have used the Neo-Epoch to retrieve a few of the original time travelers, or trained some new heroes, and sent them to the DBT with a time-egg to defeat the Time Devourer and save the universe.
The problem is Belthasar wanted more than that; he wanted to save Schala. Under normal circumstances, this would be a noble endeavor, but the existence of the universe was at stake.
Belthasar designed an unimaginably complex plan to save Schala: Project Kid. This plan necessitated the abduction and enslavement of the residents of Dinopolis and Chronopols, the perversion of the Dragon God and the disruption of civilization in the Dragonian Dimension, and untold generations of hardship, cruelty, and death predicted and initiated by Belthasar. It is also possible that he betrayed the original time travelers and orchestrated the fall of Guardia to meet his ends.
Chrono Cross also implies that Serge facilitated or hastened the completion of the Time Devourer. Thus, Belthasar put the entire universe at risk to save Schala by causing Serge to be born.
There is no way saving Schala can justify Belthasar's actions. His motivations were completely selfish and he committed immeasurable atrocities without any apparent consideration or remorse. Project Kid was nothing more than the premeditated slaughter of millions of innocent humans, dragonians and demi-humans. I would expect this sort of behavior from Magus as his wost, as it is diabolical, villainous and despicable.
Hmmm... now that is an interesting point I had never considered. I most often would think of Belthesar as almost an undeniably righteous king, and a high lord of Zeal yet untainted by the touch of Lavos. His fight against the Queen hints that his motives for things were not selfish... but yet again, he might only have wished to preserve his home. You certainly make valid points and, upon outward consideration, it does indeed seem that he is a villain who strives for a single goal at the cost of all others - which could make him a potent foe if ever crossed. Yet he is a lord and master of Zeal. By this, I think he is far more wise and cunning than near any other in any age, and nothing within his plan was not done without care or consideration - I wager there were reasons and intents behind the things that we can only guess at. I do not think his nobility should really be questioned, not so long as we do not know his full and entire purpose as he did.
Moreover, I think you are accounting a measure too much to his hand. He never intended for the abduction of the Reptites, for example. That was an act of the planet, and beyond his control or foresight. The abduction of Chronopolis... curses, I think my memory of the game is going. It has been far too long since I last played it, I think, and my understanding of the various theories and incidents has slipped. I used to know all this stuff like the back of my hand; now I can't remember even the reason for which Chronopolis needed to be pulled back. The Time Crash was what allowed Lavos to draw back Chronopolis, right? Well, if that's the case, then Belthesar could be responsible for that. However, it may well be that the researchers knew the possibility of it - but we cannot be sure. This should not be considered a sin if we do not know the fullness of it. And, as I have said, Dinopolis cannot be accounted to his hand: he did not expect it to happen, I do not think, and the war between the two was unintentional. Now, the creation and enslavement of El Nido also cannot be looked at as a sin of Belthesar's. He may indeed have set it up, so that things could go according to his purpose, but remember: those villagers who were under the enslavement are the decendants of those researchers who willingly put themselves under FATE. If anything, the choice and judgement is upon their heads, not that of Belthesar. Furthermore, the perversion of FATE and the Dragon God was an act of Lavos, not Belthesar. He may have known it would happen, it is true, but to directly counter the will of a being such as Lavos... I think that was even beyond the power of Belthesar. He needed to be cunning, and perhaps there simply was no way to save FATE from the influence of Lavos... save for the Prometheus circut! Aha, see! He did attempt to counter it. And the fall of Guardia... well, his part in that matter is only speculation. Likely he knew about it, perhaps he could have averted it... but it would be quite foolish to assume that just because he could, he should. Non-action is not neccessarially a sin, especially if one knows that through action a greater evil will come about. What this would have been... who knows? But obviously Belthesar was very careful in his changes, what he allowed and disallowed.
All these things were orchestrated by Belthesar, it is true, but it was not some grand plan, but rather a grand orchestrated battle. He was only precariously in control, and in all likelihood even his dauntless mind could find no other way by which any form of victory could be achieved. Thus at needs he conceded some thing to Lavos, allowed others to be, but always and ever worked with a subtle hand to assure that in the end things would work out the way he wished. Like a giant game of Chess. One at needs must lose pieces to victor. And one cares overmuch over every single piece, the entire game is lost. Both Lavos and Belthesar were good at this chess... but Belthesar was the better and, I think, grieved even over the neccessary loss of a pawn. And if he had directly fought and tried to change things, he would have lost. He did what he could, and Project Kid, the only way, required all the intrasices. He is justly proud of it.
Personally, I think he felt a solemn duty to rescue her, for she was his liege-lady of old.
Have I proven my point and vindicated the ancient lord?