A lot of the seemingly "weird" choices actually come down to whether or not you picked up the subtle hints. For example, someone argued that breaking up the Jedi romance on Tython was a weird choice and that both options (to lie and let them keep their relationship or break them up) are morally ambiguous. On one hand, romance is against the code, yet a romance encourages social interaction and the creation of a good bond of trust between the two.
However, Bioware made it obvious that choosing to break them up was the lightside option by demonstrating that the lovers' relationship has led them to attempt to bargain for the PC to lie to Jedi Masters as well as claim that the Jedi doctrine is absolutely wrong if they can't be together. Right then, the player can assume that the two padawans value each other over the Jedi Code, which is the main reason why romances were banned in the old Jedi order - to prevent attatchments that could cause conflicts of interests.
Back to this situation, it's clearly shown that the woman willingly left her husband. To make her go back would be a deliberate breach of her rights as a free being to choose what she wants to do within reason. Not only that, but the middle option also allows the PC to tell the truth AND get lightside points. Yet, I haven't picked it, so I wouldn't know what the ultimate outcome of that decision would have been.
Also, Jedi do manipulate and lie to certain degrees, so long as it serves the greater good. Examples of this would be Qui-Gon Jin and Obi-Wan using mind tricks and half-truths.
This is as an excellent point, and I agree with you wholeheartedly. This argument is clearly superior to the "domestic violence" argument -- if I recall correctly, the whole reason Ria deceived her husband was more or less to avoid hurting his feelings. It would be odd if she were trying to avoid hurting her abusive mate's feelings, I think. You're also right in that after talking to Ria and telling her that you'll lie to Nik, you can tell Nik the truth -- which not only nets you lightside points but convinces him to accept reality and move on. It's the best choice, if do say so myself.
That aside, the game's treatment of matters like this -- especially those relating to honesty/lying -- is in fact somewhat inconsistent. Here, lying, even when in reality it would probably be psychologically detrimental to Nik, is considered a light choice, but in the Senator Kayl mission, lying (even when it would presumably be beneficial for Coruscant in the longrun) is decidedly a dark choice. So a lie with longterm negative consequences is light and a lie with longterm positive consequences is dark. Kind of silly.