Image Source: Google
In a word, yes.
Thanos is toast ? cut horizontally the way Fury likes it.
However, the Ancient One defeating Thanos would require circumstances that are very unlikely to occur. Thanos would have to confront her one on one. In that instance, she could do what she did to Hulk in Endgame and separate his soul from his body. After that, cutting his head off would be as easy for her as preparing toast the way Fury likes it is for us ordinary humans. I?d love to know what they would say to each other before she ends him.
The most likely scenario is that the Ancient One would not face Thanos one on one. There is a reason why Thanos sent Ebony Maw after the Time Stone. He likely knew that the Sorcerer Supreme wielded it and that he would be vulnerable to his or her array of magical long-distance attacks if he couldn?t immobilize her arms. That is something Maw could do with his telekinetic powers.
My answer also presupposes that Thanos is facing her without the aid of any Infinity Stones. It?s the only way to make a fair comparison. Thanos, without any stones, would avoid facing the Ancient One alone unless he was accompanied by his children, especially Maw, and the massive army at his command. I?m giving him credit for being a master tactician that honed his tactics conquering many planets. He would know that he was a bad matchup alone against someone of her magical abilities. She has demonstrated her prowess by effectively defending the stone for centuries.
Addendum: Though Thanos indeed beat the Ancient One?s successor in a one on one fight during Infinity War, Thanos was also already in possession of 4 Infinity Stones when that battle took place.
Notice that in the second image, two of the Stones are glowing with power as Thanos resists the magical bands cast by Doctor Strange?s multi-shadow clones. The color of the bands changes from yellow to purple, indicating the stones overcoming the magical hold of the bands. (Anyone knows which stone beside the Power Stone is being employed? Looks like the Soul Stone, right?)
The possession of 4 Stones gave Thanos a significant power boost as well as the ability to repel magical attacks. Without them, he?d be defeated one on one versus Doctor Strange on Titan. That said, if the Ancient One did square off against Thanos (with four stones) on Titan in place of Doctor Strange, she would also lose that battle. The fight itself, however, would be visually spectacular. She?d employ a different set of favorite spells, but the outcome would be the same.