Thiel actually explained this in a talk when I worked there. It comes from Lord of the Rings which Peter Thiel is very fond of. Apparently the Palantiri aren't inherently good or bad, it's just that power's impact reflects the people who use it. The ancient elves or wizards or whatever used them for good. But Sauron got his hands on one and used it for bad. The sinister potential was a deliberate choice, to remind people to be sure that power isn't abused. Actually kind of a good message for the tool Palantir builds, but probably not good for PR.
Also Thiel is very consistent on using Tolkien's pronunciation. It's not PA-lan-tir. Or Pa-LAN-tir. It's pa-lan-TIR with emphasis on the last syllable. There's actually a written accent in the books: http://tolkiengateway.net/wiki/Palant%C3%ADri
Regardless everybody at the company sad PA-lan-tir.