Just like the question indicates — why did Merope name her son after her father, who constantly terrorized and abused her?
When Dumbledore is teaching Harry about Voldemort's past, we see that Merope was terrorized and abused by her father — in fact, Marvolo terrorizes Merope so much that it shows physically.
[...] but Harry thought he had never seen a more defeated-looking person. -Harry Potter and the Half Blood Prince, Chapter 10, The House of Gaunt
And then we see that Marvolo abuses Merope verbally.
"Pick it up!" Gaunt bellowed at her. "That's right, grub it on the floor like some filthy Muggle, what's your wand for, you useless sack of much?" [...] Gaunt screamed, "Mend it, you pointless lump, mend it!" [...] Instead, [Marvolo] jeered at his daughter, "Lucky the nice man from the Ministry's here, isn't it? Perhaps he'll take you off my hands, perhaps he doesn't mind dirty little Squibs..."
We also learn that Marvolo doesn't mind causing Merope physical discomfort.
[...] [Marvolo] was dragging [Merope] towards Ogden by a gold chain around her neck [...] shaking the heavy golden locket at [Ogden], while Merope spluttered and gasped for breath [...] "Mr. Gaunt, your daughter!" said Ogden in alarm, but Gaunt had already released Merope; she staggered away from him, back to her corner, massaging her neck and gulping for air [...] "You disgusting little Squib, you filthy little blood traitor!" roared Gaunt, losing control, and his hands closed around his daughter's throat.
These pieces of evidence clearly state that Merope was being terrorized and abused by her father, Marvolo. And yet we see that she specifically states that she'd like her child to be named after Marvolo:
and then she told me he was to be named [...] Marvolo, for her father [...] -Harry Potter and the Half-Blood Prince, Chapter 13, The Secret Riddle
So, why does Merope insist on naming her child after her father, when he has terrorized and abused her?