MACUSA closely monitors all magic used.
Though Newt, Tina, and didn’t want Jacob to be Obliviated, it’s unlikely they could have tried to stop it without MACUSA catching them. MACUSA monitors all spells cast in America through a map kept on a wall in the Major Investigation Department. Tina would know that, and Queenie possibly might as well, so they’ll know they can’t try to prevent Jacob from being Obliviated without MACUSA knowing.
“Foremost of these is the Major Investigation Department, MACUSA’s centre of control and Graves’ personal fiefdom. On the wall of the department is a map of North America that twinkles every time a spell is cast, pinpointing exactly where.
‘It will only be seen very briefly in the film,’ admits Mina, who nevertheless conceptualized an entire backstory for how the map is being used to spy upon wizard freedoms.”
- Inside the Magic: The Making of Fantastic Beasts and Where to Find Them
In addition to the monitoring of all spells cast in America, it’s likely that what happened to Jacob would be watched especially closely. Madam Picquery knew that they were having trouble letting Jacob be Obliviated, and was also insistent that he needed to be.
“MADAM PICQUERY
Is that No-Maj still here?
(on seeing JACOB)
Obliviate him. There can be no exceptions.
MADAM PICQUERY reads the anguish in their faces.
MADAM PICQUERY
I’m sorry – but even one witness . . . you know the law.
A pause. She is uncomfortable at their distress.
MADAM PICQUERY
I’ll let you say goodbye.
She leaves.”
- Fantastic Beasts and Where to Find Them (The Original Screenplay)
It’s likely MACUSA would have been watching to make sure no one tried to escape with Jacob. Aurors were right outside the subway where Jacob was supposed to exit into the rain.
“JACOB leads the others up the steps of the subway, QUEENIE following close behind him.
Rain is still falling heavily, the streets now almost empty but for a few hard-working Aurors.
JACOB has reached the top of the steps and stands, gazing into the rain.”
- Fantastic Beasts and Where to Find Them (The Original Screenplay)
Newt, Tina, and Queenie likely realized there was nothing they could do without MACUSA finding out, punishing them, and still Obliviating Jacob despite their best efforts to prevent that from happening.