I think Helen's using a version of "Tough Love" on Locke. He needs to care about something more than getting the father who left him to be raised an orphan, conned him out of a kidney, told him to his face that the only reason he acted as he did (the plaintive, "Why?" question from Locke while parked in his Volkswagen) was "because you had something I wanted. Other than that, I didn't care if you lived or died." (or words to that effect).

Locke promised Helen he'd stop stalking his dad. He lied. She caught him at it. At the start of Lockdown, Locke and Helen are living together, he's saved enough to buy a ring...and then...his dad again. Surely, you can see that she afraid this will undo all the progress Locke's made in getting past his father's betrayal. I know some people who have attempted suicide at the death of their estranged fathers. Now there is absolutely no chance for reconciliation and they can't live with that knowledge. In the back of their heads, they were still hoping that somewhere, someday, the dad would show up and be the dad they always fantasized having. They can't live in a world without that hope.

I think Helen thinks John is still fragile and when she discovers the dad's alive and working yet another con involving John, she explodes (and, perhaps, concedes defeat and leaves John standing in the parking lot).

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charlie98210
"Whoa!" she said. "Cry 'Havoc!' And let loose the dogs of war!"
And, like Banquo's ghost, they just won't go away.