Black, an evil neurosurgeon, wishes to see White dead but is unwilling to do the deed himself. Knowing that Mary Jones also despises White and will have a single good opportunity to kill him, Black inserts a mechanism into Jones’s brain that enables Black to monitor and to control Jones’s neurological activity. If the activity in Jones’s brain suggests that she is on the verge of deciding not to kill White when the opportunity arises, Black’s mechanism will intervene and cause Jones to decide to commit the murder. On the other hand, if Jones decides to murder White on her own, the mechanism will not intervene. It will merely monitor but will not affect her neurological function. Now suppose that when the occasion arises, Jones decides to kill White without any “help” from Black’s mechanism. In the judgment of Frankfurt and most others, Jones is morally responsible for her act. Nonetheless, it appears that she is unable to do otherwise since if she had attempted to do so, she would have been thwarted by Black’s device. (Adapted from an example by John Fischer, 1982).

The argument is that Mary used her freewill to kill White even though she had no possible alternatives. This is supposed to be a counterexample to the Principle of Alternative Possibilities (PAP) that I use do defend determinism in light of divine foreknowledge. Here’s my argument formally:
1. An action A is not free if one cannot choose an alternative possibility (PAP)
2. God’s foreknowledge of an action A eliminates all alternative possibilities.
3. Therefor action A was not chosen freely
The example above supposedly refutes premise 1 by giving an example of an action that is freely chosen even though no alternative is available. The first problem I have with this counterexample is that it assumes freewill a priori. If the universe is truly deterministic then Mary didn’t freely chose to kill White. No alternative was available to her not because of Black’s device, but because of the nature of the universe.
There is also a logical problem with the counterexample. This time, let’s presuppose freewill. I would argue that Mary did have an alternative possibility. She could have chosen not to kill White, even though that choice would be immediately overridden by Black’s device. There were alternative possibilities with respect to Mary’s choice even if there wasn’t with respect to her action. Thus PAP is intact.
The third problem with this counterexample is a theological one. It suggests that God’s foreknowledge actively overrides any alternative choices we make. This would imply that God overrides some people’s choice not to torture, kill, etc. and even override some people’s choice to accept Jesus. This would contradict the grand benevolence attributed to God by Christianity.

A Molinist would say since agent A, when placed in circumstance C, will freely choose option X over option Y, God ordains circumstance C.

This really sounds like linguistic trickery to me. The statement is completely consistent without the word ‘freely’. It’s almost as if it is inserted by the Molinist so (s)he can claim, “See, the choice was free. It says so right there”.
It’s not true freedom. To be truly a ‘free’ choice, agent A must be able to choose Y in circumstance C. If it is guaranteed that A will choose X given C, it is improper to describe that choice as ‘free’. That guarantee is made by God’s foreknowledge.
Also, building on what Snurp wrote, since God knows every choice every agent will make in every circumstance and God ordained every circumstance, the universe de facto deterministic.

An intellect which at any given moment knew all the forces that animate Nature and the mutual positions of the beings that comprise it, if this intellect were vast enough to submit its data to analysis, could condense into a single formula the movement of the greatest bodies of the universe and that of the lightest atom: for such an intellect nothing could be uncertain; and the future just like the past would be present before our eyes

Where I would disagree is that this is not a forgone conclusion. There are areas of modern physics that concede there are exceptions.
For most things, we observe that an object is in its present state because of the values of its measurable proprieties and vice versa.
Water exists as steam because the temperature is 212F, pressure and volume remaining standard. Therefore, any water measured at 212F with standard pressure and volume is steam.
Some things in physics cannot be completely measured. Quantum particles can have their position or velocity measured, not both. The state of a quantum particle can only be described as the position and probable velocity or velocity and probable position.
How does all this relate to free will?
Calvinism would say God knows person P in circumstance C will choose option X over option Y, therefore God ordains A to choose X. A Molinist would say since agent A, when placed in circumstance C, will freely choose option X over option Y, God ordains circumstance C.
The former has God ordaining choices whereas the later has God ordaining circumstances.