Before addressing the article itself, lets first note that news writers have known for more than 80 years that the addition of the name Einstein to the headline will increase the number of readers. And we aren't just talking about your supermarket tabloids, the mainstream press has been using this for years too.
I'm not sure what your point is here, it's lost on me. When considering gravitation, Newton and Einstein are by far the most relevant names associated with the subject, having themselves published the two most widely used formulations of the gravitation field in the last 400 years, namely, F = GMm/r^2 and the Einstein Field Equations, published in 1915. So it's entirely proper to bring their names in to an article headline when considering evidence that these two masterful successive explanations may not be quite up to the task.
So beyond the fact that this article has to be approached with a massive amount of skepticism... what do the facts point to? Well, what did the article say?
"The anomaly officially materialized in 1988, 16 years after NASA launched Pioneer 10 toward the outer planets."
Really? Well, if it wasn't effecting the entire voyage of the spacecrafts, I think we can safely rule out issues with our understanding of gravitation.
Again, I'm totally lost on what you're trying to say here.
One can explain the motions of 7 out of the 8 planets in our solar system using Newton's equations alone, and have a fairly good stab at Mercury's orbit too. Long before Einstein suggested revisions to gravity and his theories of relativity, people were perfectly satisfied that their motions had been explained almost exactly by Newtonian mechanics.
It was only when more precise measurement techniques and more evidence had been gathered and new experiments had been devised that scientists saw there may be scope for revision, relativity emerging from problems with electromagnetic field theories of the late 19th century, and the Einstein field equations for gravity arising out of these.
We
know our explanation of gravity is not complete, because we can't explain what happens at Event Horizons of black holes (and how quantum theory relates when small and large scale physics collide).
The Pioneer anomaly could well be evidence of our theory breaking down at the edges, much as Newton's theories broke down when trying to explain new experimental evidence leading to Einstein's work. It could very well be the case our current theories are good approximations that don't explain edge cases, and that experimental data like this might be key to a better theory.
Don't assume that our understanding of anything is perfect and timeless, especially when NASA put Newton, not Einstein, in the driving seat for the vast majority of their intersolar missions because the effects of the EFE revisions are so small they are barely measurable at any reasonable precision or scale, especially when talking about the inexact nature of space probe missions (which have surprisingly high degrees of uncertainty in orbits, slingshots, and so on).
And the Pioneer spacecrafts were the first to start reaching the boundaries of our Sun's influence. We know that the Sun is moving through space, but we have almost no idea what the interstellar medium might be like. Or how it might be moving relative to our solar system.
Dude, you should read up on the Michelson–Morley experiment. The ideas of a luminferous aether (interstellar medium) went out in 1887.
Read
A Brief History of Time or one of the countless other layman-orientated books on modern (astro)physics if you're interested.
As for scientific journalism, there will always be a place for slightly sensationalist articles like this, even if they say nothing substantive. The bleeding edge of physics is nearly impossible for the average man to grasp, but we must continue to try and make it accessible, otherwise we'll simply lock physicists in an impenetrable ivory tower that will not only serve to discourage youngsters from joining the field, but will also discourage adults from listening to the important results that physics produces from time to time.
My point is, though, don't roll your eyes at an article because you consider it to be overly summarized or sensationalist, if you want to read the academic paper, then do so, but you can't expect everyone else to do so and understand it. This is why
New Scientist sells more copies than
Nature, and a
Brief History of Time is a NYT bestseller when
Gravitation by Misner, Thorne, Wheeler & Wheeler lies at the bottom of the proverbial physics bargain bucket.