A beta reader of sorts (cousin) mentioned he thought my MC2 rather brutal in her capture of MC1 - though justified. 

I have her dupe him into surrendering (believing himself outnumbered and outgunned). Once he does surrender, she does the following:

* searches him
* disarms him
* handcuffs him
* binds his elbows to prevent escape
* rigs a chokehold out of a dog leash
* threatens him with a hunting knife
* holds him at gun point
* threatens to geld him (psychological tactic only)

She is successful in convincing him that any unsanctioned movement is a bad idea. She uses these tactics because she is smaller than he is and she would lose in a fight. She cannot allow him, at that moment, to consider resisting. 

Has she crossed the line between using justified force to bring in a dangerous prisoner and brutality?

It occurs in Bolivia shortly after an assassination.

To clarify somewhat, she does not go directly to the choke-hold or threat of castration. MC1 asks her something that makes her choose to go further as he is not in the mindset she wants yet.