Spec Ops: The Line was released in 2012.
Breaking Bad started in 2008.
Thus, if you must insist that one one inspired the other, then Breaking Bad was the inspiration for Spec Ops: The line. However, it isn't that simple. Just because it appears that the protagonist goes bad, doesn't mean the story lines are at all similar.
From that Wikipedia Page on Spec Ops: The Line...
While lead writer Walt Williams has stated that there are many influences, the premise is inspired by Joseph Conrad's novella Heart of Darkness, with Konrad replacing Kurtz.
Or, if you need a more recent influence... Apocalypse Now.
The idea of a good man sinking deep to perform questionable acts in order to maintain the "Greater Good"... regardless of whether or not that is a questionable good itself... is not a new one. Our Hero in Spec Ops: The Line is pursuing a villan.
In Breaking Bad, our protagonist is beaten down by the events in his life, and he makes a choice to turn bad, as he sees it as his only way out. He proceeds to be bad, and get badder, while attempting to maintain some semblance of still fitting in to society's concept of being good, or doing as he is supposed to. Unfortunately, the character of Walter started teetering on the edge of being morally questionable very early on. His trip over the edge was by choice. He wanted to go down the wrong path; he takes pride in what he does and how he does it.
If we were going to compare protagonists and their stories... and we needed a single setting to do so, then Apocalypse Now is a pretty good stage to work from. You could compare Captain Martin Walker from Spec Ops:The Line to Martin Sheen's character, and you could compare Walter White from Breaking Bad to Marlon Brando's character. Both characters could be in the same story, but I don't see how you can say that both characters are the same (or inspiration for one another).