All the non-W:tA elements will be out of the setting, yes. For instance, there will probably be vampires, but they will be faceless antagonists of whose internecine politics and divisions the Gaian sorcerers are almost completely ignorant. I'll probably change a bunch of vampire mechanics just to keep my players on their toes.
There will be Pentex. I love Pentex. My home wifi is named Pentex. Whether it will have a connection to vampires, I'm not sure; that always struck me as a little bit strained.
The "good" sorcerers, as an overall group, call themselves the Nation of Gaia. It's a secret society and I need to figure out its internal organization. There are probably families all of whose members are part of the Nation, but they would constitute an ever-shrinking percentage of the Nation's membership.
Anyone smart and dedicated enough can learn sorcery, but shamanism requires a calling from the spirits, and psychic abilities are innate (trainable but not teachable). All three types serve the Nation.
How new members are recruited is one of the things I haven't decided yet. Ditto factional politics, because I don't know what the factions are.
I'm not sure how the government fits in. How does it operate in a regular W:tA game?
Yes, the Gaian sorcerers can enter the Umbra, but I'm thinking it requires a ritual, not just "stepping sideways"; it may be more like astral projection than physical travel. There are caerns, I think, just as in W:tA, and groups that guard them; the "sept" terminology will need revision, but picking new names for things isn't hard.
Someone on IRC brought up the point that, in regular W:tA, going Crinos and wading into the enemy is actually pretty dumb; smart Garou stay in Homid and use sniper rifles and body armor, because fomori usually have silver or Wyrm-toxins or other sources of aggravated damage available. On the other hand, going Crinos and wading into the enemy is cool. What can I do to promote it?