So here's my personal take on this question.
TL;DR: Agatha has taught herself control over her siphoning ability, but it isn't perfect control, and certain extenuating circumstances can lead to a loss of control.
Despite her penchant for lying whenever it suits her, I tend to believe Agatha when she says she couldn't control her power (specifically, back in the Salem days, and then after Alice's death). These are both highly emotionally charged situations where Agatha is being actively, physically threatened. Agatha's siphoning ability is at its core a defensive power, something meant to protect her from harm, and it seems to be able to kick in involuntarily.
The act of absorbing power also appears to be extremely pleasurable, and likely addictive. Whether this is direct physical pleasure or just the emotional rush of feeling powerful and untouchable, it's hard to say. But it's clear that Agatha greatly enjoys the act of siphoning, to the point where she continues to do it even when it draws unwanted attention from her ex-wife.
I also think Agatha genuinely believes, largely as a result of her past trauma, that killing other witches is a matter of survival. As she expresses to Nicky, it's either kill or be killed. Is that necessarily true? Maybe not. But in Agatha's mind, the only way for her to survive is if other witches don't. No one can hurt her if they're all dead.
To answer the original question, I think Agatha taught herself control over her ability sometime in the centuries between her original coven's death and the events of Wandavision.
Now, I don't believe that this was for any moral or ethical reason, or any concern about the lives of other witches. No, instead Agatha is motivated by knowledge, power, and survival (and Nicky, when he was alive). And I can't believe there's any way that someone like that would be comfortable having a power they couldn't control. Surely someone who has spent centuries perfecting their craft would be highly motivated to master their own innate abilities as well. So Agatha did. She took the time over the centuries to slowly learn how to stop siphoning at will. We've seen her demonstrate this with Billy, and I highly doubt this was the first time she'd ever stopped herself (though it may be the first time she did so for the purpose to sparing someone's life).
That said, it's not a perfect control. We see, with Alice's death, that Agatha can still be overwhelmed by her ability in the right circumstances. (She's already emotional vulnerable from Rio's presence, and then the ghost of her abusive mother literally takes control of her body, and then magic is being blasted at her body before her mind has a chance to catch up.)
In my opinion, the emotional vulnerability we see from Agatha after that trial is not so much about the guilt over Alice's death (though it's possible there's a little of that), but rather a reaction to having lost control over her power in a way that probably hasn't happened in decades. She's already been feeling vulnerable after Wanda stole her power and fucked with her mind, and this new loss of control makes it even worse. Not to mention, it puts her in a precarious position with the other coven members, who may now be motivated to hurt her, and that's a familiar and terrifying place to be. Is it any wonder that she pivots so hard into callous and uncaring Agatha when confronted by Billy?
(Wow that got long. Can you tell I've thought about this before?)
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