I actually wondered the same questions when I took an interest in becoming a mason. Upon asking the same questions, these were the answers i received.
1. Why is there a Judeo Christian bible sitting on the alter in many lodges and why are we using it to take our obligations on?
From my understanding, based on the majority of the lodge's religious beliefs determines what actually sits on the alter. While the Bible may be on the alter in one lodge, the Quran may be in another.
2. Why have some "elders" referred to the "G" above the WM head as "God" and some "Geometry"?
From what I gathered, this is a minunderstanding. The "G" actually stands for "Geometry" however many take it or assume it as "God", which it in fact alludes to but doesn't stand for. I can't really think of an easy way to explain it at the moment, but the "G" represents geometry, which means a form created based on its elements, masonically meaning the universe (form) created by an element (a person's god or deity of choice). So while the "G" does in fact stand for "Geometry" it also does stand for "God", but it stands for each individual person's "God" (deity), not a certain named diety "God".... I think I just made this more confusing
3. Why is a belief in Deity a requirement, if this is not a religious organization?
I know exactly what you are saying, but this isn't a question, this is a debate. This can be argued so many ways. Based on understanding and interpretation alone, a diety is a belief in some defined force that controls an aspect of life or a world, while being religious is to love and respect a diety. I'll stop right there on this one because I know where it will lead. This is a good debate for a new thread though!
Matt