This is how John Titor sums up the Grandfather Paradox and its effects in the Steins;Gate universe (from the episode 2 English dub):
Someone else: Aren't you worried that by being here you're creating some kind of a paradox?
John Titor: Ah, the so-called "Grandfather Paradox"? It doesn't exist. It's possible to meet your past self. You'll simply change world lines if you do.
The anime doesn't really touch on it; the details of the time machines that John Titor uses are not really revealed. They're touched upon by the mechanics of the show, but never detailed in dialog, which could lead us to assume that this is a plot hole. As someone else put it, "The wrong explanation ... probably makes more sense on the surface than what the truth is."
However, the Steins;Gate visual novel goes a bit more in-depth. Firstly, Titor explains that these events make perfect sense:
"Cause and effect will be reconfigured. The me sitting here will disappear, since I'd probably be living peacefully in 2036." – Suzuha
Additionally, Okarin determines a bit more about the mechanics of the time travel:
By the way, about what will happen if I meet the "me" that already returned once-- in other words, the me that stabbed Kurisu to death, I already asked Suzuha beforehand.
The conclusion is that "we won't meet."
The world line where I already killed Kurisu is minutely different from where we're time traveling to.
Meaning time travel slightly changes the world line divergence ratio.
Though of course, that value is still within the error range of the attractor field, so it can't make any concrete changes.
In my opinion, this explanation is a bit wishy-washy, but it's canon; essentially, he's saying:
Using the time machine creates a slightly different world line, so there will not be conflicts in repeated time travel attempts. (It "overwrites" the previous attempt.) But then, the two world lines merge within the attractor field again.
In essence, we can more-or-less explain the events (using one last spoiler tag) in the following way:
Suzuha disappeared because, even though she existed on a slightly separated world line, when she traveled back to the future, the two lines would again merge and her existence would be overwritten by the Steins Gate world line.
I would conclude, then, that the events that took place in the last episode do not violate the Grandfather Paradox. There is sufficient evidence to show that the world line's future has been altered in such a way as to justify the events.