I would not say she hold a torch for Logan, more like a mix of friendship and attraction and she was open to talk about this right before they got married, this was honestly one my favorite issues with them back then, because they didnīt shy away from talking about the unsavory aspects of their relationship before taking a step to make their compromise official, I miss those kind of thoughful issues in which we get into the characters head and know their reasons.
Now outside story, I think Morrison just added that scene between Logan and Jean to make more palatable the plans he had for Emma and Scott and then went even more overboard saying Jean bassically put them together so it was alright Scott stayed with Emma when still it didnīt feel that way for a long time for fans or the other X-men characters.
All this I think would be worth talking about between the characters, I think a little touch of them talking about their issues in a mature way without avoiding the harder matters would do wonders for their relationship and would be an interesting narrative. Itīs great to see them kissing and playing rock, paper, scissors sometimes but those are characters with a lot of background to cover before getting back into bussines as usual when it comes to their relationship and making it seem like they donīt looks false to long time readers of both characters.