Any acknowledged consideration between the treatment of 'Gone Girl' in light of the Oscar Pistorious case?

NO

There is no sourced evidence that the circumstances surrounding the Oscar Pistorious case had any influence on filmmakers.

HOWEVER

There is evidence that it was based to some degree on the Scott Peterson case. Author Gillian Flynn and the film's director, David Fincher have both made references to Scott Peterson and the circumstances surrounding the events of the case.

While Gillian Flynn denies that Nick Dunne is based on Scott Peterson, she does refer to him in an interview with Entertainment Weekly:

I definitely didn’t want to do anything specific. One could point to Scott and Lacey Peterson — they were certainly a good-looking couple. But they’re always good-looking couples. That’s why they end up on TV. You don’t normally see incredibly ugly people who’ve gone missing and it becomes a sensation. It could be any number of those types of cases, but that was what kind of interested me: the selection and the packaging of a tragedy. In a way, I reverse-engineered some of it. What’s going to amp up the media’s interest in this, and what’s going to make it believable that the media’s going to descend on this?

The Scott Peterson case had more of an influence on David Fincher while making the movie. In a 2014 interview with Playboy, Fincher states that the Scott Peterson case was a jumping off point:

There are certainly a lot of elements in Gillian’s book that are well trod in my movies, like the procedural aspect, people putting together clues and things like that. It’s also a very naughty book. But my thought when I first read it was, Fuck, how do you throw away two thirds of this and still end up with the same journey? How do you still play with the Scott Peterson aspect [the notorious case in which Peterson murdered his pregnant wife]—which we all know is the jumping-off point —but make it about something bigger and more universal?

According to a 2014 Vanity Fair article, Fincher decided to cast Ben Affleck after googling his nervous smile. He compared his looks and demeanor to that of Scott Peterson during the time that Peterson was holding candlelight vigils and "helping" investigators find his wife:

Is that the smile of an innocent man? In the same interview, Fincher goes on to discuss the theme of public perception that runs throughout both the book and the film. He draws a comparison to Scott Peterson, a man whose uneasy demeanor made him guilty in the public eye long before he was actually convicted of murdering his wife.

When describing Ben Affleck (the lead actor in the film), Fincher states:

Who looks more like Scott Peterson than Ben Affleck.

You can see the physical similarities with this picture showing Ben Affleck on the Left and Scott Peterson on the Right:

"Has Fincher (or even Gillian Flynn, who wrote both the novel and the screenplay) discussed the thematic similarities between the text and the case?"
There is no evidence supporting Fincher discussing any similarities between the screenplay and the Oscar Pistorious case. There is, however, plenty of evidence supporting the similarities between the screenplay and the Scott Peterson case.

Firstly, you have failed to look at the times frames involved. Oscar killed Reeva on the 14th of February 2013.

Gone Girl was in the works a long time before the murder

"Gone Girl is a film adaptation of Flynn's 2012 novel of the same name, and the author also wrote the adapted screenplay. One of the film's producers, Leslie Dixon, read the manuscript of the novel in 2011 and brought it to the attention of Reese Witherspoon in December of that year. Witherspoon and Dixon then collaborated with Bruna Papandrea to further develop the manuscript—with Flynn's film agent, Shari Smiley, they met with film studios in early 2012.[6]

Flynn submitted her first draft screenplay to 20th Century Fox in December 2012, before Fincher was selected as the director for the project."

So if the first draft of the screenplay was submitted 3 months the prior to oscar killing Reeva, and the screenplay was based on the book, I find it highly unlikely that they would have decided to change the screenplay and let it be affected or influenced by a murder which would only be tried in court after the movie was filmed.

Secondly, Fincher started filming in Sept 2013 for about 5 weeks. The details of Reeva's murder were not fully explored until the trial started in March 2014. It was live coverage of the trial which pushed the story into worldwide media exposure.

Third: The murder of Reeva is by no means unique and there are many other cases that spring to mind like the OJ Simpson and Scott Peterson trials. Regardless of how long ago these famous trials and murders occurred, their themes still play out in popular culture and daily references. Any murder of a girlfriend or spouse with a public figure involved is going to play out in the media in the same way. All famous trials are going to resonate in some ways.

You have to ask David Fincher to give you an absolute answer, but my conclusion is it is highly unlikely that he would have seen the need to make the movie resonate with the Oscar Trial. Or to use your words, I doubt he needed to or was influenced to 'play up' any thematic similarities.

And before you ask this question in the future years to come: no, I don't think the director of the one day to be made Oscar Pistorius biopic will be influenced into introducing thematic similarities from Gone Girl.