I didn't see Time as a villain.
In Marketing, and more specifically the soon to be dead Disney Infinity (RIP), Time is shown to be a Villain/Bad Guy. In fact, those who play Disney Infinity were introduced to him via a Boss Battle... So, I just assumed he was the main villain in this movie...
Even though he does act sort of antagonistic towards our protagonist, Alice, he is in no way evil. It's his job to keep the timeline stable, of course he wouldn't give away the Chronosphere.
Even our main villain, Ol' Queen Big Head gets redeemed in the end, but I never felt that Time was ever malicious or malevolent like Iracebeth was.