Option 1: Terrorist IDs available to a small group of players we all can identify easily, who can be held accountable collectively, and who risk losing access to said ID in the event of poor behaviour
Option 2: Everyone on the server can get a terrorist ID
Option 3: We remove anything resembling terrorist ID
At present, Option 1 is what exists.
(Of course the factions you mention aren't terrorists, but merely factions who happen to have IDs which are not freely available. Considering the Coalition, say, is opposed to all the Houses of the Alliance, it would be chaos on a disproportionate scale.)
Using the word "indie" doesn't make sense here. You can't be an "indie" Keeper; by definition, "indie Keepers" don't/can't exist.
Possibly you apply for a faction and get accepted or not? Membership of any faction does not exclude you from being a tool, nor does it mean you are a tool. Behaviour decides that.