I don't really think the marks in and of themselves are extremely significant. The mark on Juliet's arm was more for Jack's benefit than anything else...just to make him feel even more connected to her. It could be a sign to her own people that she is working as a double agent, or it could mean "I'm With Stupid"
I think the producers are just throwing around some mysterious looking symbols to keep us distracted. I doubt it was an actual scientology symbol (upside down at that), because then they would have to deal with lawsuits and such.....
The mark on the tree served a useful purpose, and they are way too advanced to just use a good old fasioned "X"