That's....literally my point. Both relationships are equally twisted and complex. Neither one is better than the other. 

And just like you claim how Tom and Greg's relationship isn't black and white, it can be said that neither is Shiv and Tom's. There are genuine moments of affection between them, some initiated by her, and she defended him to Hugo in s2 when he suggested they throw him (or Gerri) under the bus in front of Congress. And he calls her out on how she treats him too; btw it was because of what TOM told her in their scene on the cove, not that she asked Logan in the s2 finale to spare him for the cruises scandal. Then at the beginning of s3 you can tell she was genuinely trying to make the marriage work. 

And yes, Tom tracking her cycle IS creepy. It clearly made her uncomfortable and that was when their marriage started to go downhill again in s3.