You can't judge Sandra by her inaction honestly. Her phobia definitely would make her getting close to anyone hard. Not to mention, it's clear she is more invested in the MC than she has been in previous guys, especially when you hear Lisa's reactions to the things Sandra lets the MC get away with (germ and dirt wise), that any one else would have been thrown out of the apartment for.
Sandra is a very compartmentalized person though. Fun is Fun, Work is Work, Cleaning is Cleaning. She doesn't like to have things mix together, so when she said she needed to work and not be distracted she was drawing a very clear line. Once again, she lets the MC get away with bothering her, something she'd probably kick anyone else out of her life for doing. If there is a break up coming, it will probably because her neurosis get the better of her and she just can't take her boundaries getting crossed anymore.
A lot of their issues are actually exacerbated by Haley. The pet name would have been fine, he would have even gotten used to it if his sister didn't constantly give him shit about it. She makes fun of every part of Sandra and the MC's romantic quirks because of her outright jealousy. She knows exactly what buttons to push on her brother to get the "Doubt about the relationship" reaction. We've seen in the most recent update that it's working and he's beginning to treat Sandra's cute and caring way of being in a relationship as mommy'ing him, when really what she's doing is fighting her own OCD/Germaphobia issues and trying to make it work with him at the same time.