While the effort to push Liara onto Shepard seems pretty clear, it can also be a matter of interpretation. Shepard saved Liara's life, so it's as natural as Tali (or Garrus) for her to be attracted to the commander. It's fine to talk to her whether or not romancing someone else, simply tell her the truth that Shepard doesn't 'like her that way'. It's appropriately awkward for the moment, but ultimately survivable.
Liara's development from a cowering prothean scientist to a more confident adventurer isn't really that abrupt if consideration is given to the fact that she spent *two years* tracking down and rescuing Shepard's body. She *had* to grow into her strengths to save (arguably) her best friend's remains from monsters. When Shepard turns up in her office on Illium, it's a natural reaction for Liara to give Shepard a happy hug. The last time she saw the commander was meat-in-a-box turned over to Cerberus. She pushes Shepard away quick enough in her zealous hunt for the Shadow Broker. By the end of that focused intention, it's a Tuesday for Shepard, but a rushing finale for Liara, and the abrupt culmination of years of deadly, careful, and strategic investigation.
As for Aethyta, she's taken charge of monitoring Liara's activities for the asari. She's making sure Liara (a suddenly powerful and frighteningly-influential broker) isn't being led astray by a friend with a shady past association with a known terrorist group. One of the most effective ways to get information is to get under someone's skin, and Aethyta has abrasive inclination as well as a lot of wry practice. She's also getting her kicks needling both Liara and Shepard about their relationship. It's no more serious than James's nicknaming folks.
Liara might be Bioware's obvious favorite, but her character development is consistent and understandable. Her romance is at Shepard's choice, and if denied, she settles for a very close and supportive friendship. Possibly a little too tight for some commanders, but she does not interfere with any of Shepard's other lovers, and lore-wise, she's asari, so that's probably not that strange for them.
Now, look at this mess, and I'm not even that big of a fan of Liara. :)