The Shivans destroyed Vasuda, and they tried to do the same to Earth, not to mention attempted annihilation of the Terrans and Vasudans. They killed the Ancients when simply crippling them militarily would have been adequate.
Given that the Ancients destroyed and subdued many other species themselves, I would consider it poetic justice. The Terrans and the Vasudans were also fighting a total war with the purpose of seemingly annihilating the other species. Since the Shivans don't communicate on the same level as most Terrans and Vasudans and since they have shown the resolve to abuse and exploit subspace, extinction of two sentient species would be a justifiable answer to preserving life throughout the galaxy. And considering that the Shivans have left the two species alone after the destruction of the Lucifer for the most part until the two species interfered, I would say that they have shown restraint as well.
The GTI may have experimented on them, but that in no way justifies what they did. The GTVA did try to invade their systems, but only after the Shivans destroyed the GTC Vigilant.
Why not? If they can view the universe objectively* and they 'know best', then they can indeed justify what they do.
And the Trinity messed with the Shivans first, not the Vigilant. The Shivans may not have been able to distinguish between the NTF and the GTVA.
They might be preservers, but only in the most horrific way possible: they preserve by commiting xenocide against any two sentient races that ever clash with each other. They've certainly done really bad things.
In the case of the Ancients, it was evident that they did not know their crimes until the very end. As for the Terrans and Vasudans, there is no evidence that there has been any xenocidal intentions after the destruction of the Lucifer, which may have signaled to the Shivans that the Terrans and Vasudans are now allied and no longer fighting a xenocidal war themselves.
But given that the Shivans have been around far longer than any species known within FreeSpace, we can assume that they have attempted to show mercy, only to see the hegemonic empire rise again. If that is the case, then xenocide may be the best alternative.
Yes, we don't know what the Vishnans really are. They might not be much better than the Shivans, but that doesn't change the fact that the Shivans are not nice people.
Shivans are not nice to the Ancients. Shivans are certainly the reason why the Terrans and Vasudans still exist.
*
Super Happies! Remember them?EDIT: What Battuta said tactfully.