He probably concluded that his father was "bewitched" or "ensnared" but this is a long way from recognizing his father as a victim. In chapter 17 of Half Blood Prince, Tom Riddle is seeking information from his uncle, Morfin Gaunt:
"I thought you was that Muggle," whispered Morfin. "You look mighty
like that Muggle."
"What Muggle?" said Riddle sharply. "That Muggle
what my sister took a fancy to, that Muggle what lives in the big
house over the way." said Morfin.
Tom Riddle seemed to value his mother slightly more, as shown in Chamber of Secrets:
You think I was going to use my filthy Muggle father's name forever? I, in whose veins runs the blood of Salazar Slytherin himself, through my mother's side? I, keep the name of a foul, common Muggle, who abandoned me even before I was born, just because he found out his wife was a witch?
Here he seems to think the only reason his Muggle father left Merope is because she was a witch. That was enough for Voldemort to side against him. Furthermore, Tom was raised in an era where men were not typically viewed as victims in cases of sexual assault. He appealed to the traditionalists in wizarding society, which further narrows the chances of him viewing what happened as sexual assault.
To recognize his father as a victim goes against Voldemort's character. If he knew Tom Riddle Sr. was taken against his will, it would not have earned his father any sympathy.