My first thought at the idea of Tommy's testimony causing a coup against Miscavige is that not many people left when the other spokescreatures (RVY or Rinder) left and spoke out about Miscavige and/or Hubbard, and some people don't even leave the cult when they're disconnected from their own children who leave, like Astra and Zoe's mother. They aren't reading news of these court events. Instead, they're working on their next level, or working on blocking entheta and clearing the planet.
For the members who didn't or don't work under him closely enough, Miscavige became Hubbard-by-proxy, the Keeper of the Source. A former Sea Ogre, relatively newly out, was asked on this board a few months ago what he thought about the absence of other executives speaking at major events and how it was mostly the David Miscavige show. He said he liked it that way. He makes Scientology appear strong and growing.
However, a few things distinguish Tommy's tenure as spokescreature, from that of past spokescreatures. He had increased TV presence, the fight with Sweeney, the walking out on Bashir, which all meant increased Internet presence also. There is his connection to celebrities including a few important ones like Tom Cruise. I'm not sure that the majority of Scientologists were even aware of who Tommy Davis is/was. So, if they do find out he testified against Miscavige, they would just think he was yet another SP or "defrocked apostate," and it really has nothing to do with the "tech" or their "religion."
I would have thought the Death Event and Miscavige's takeover would have spelled the imminent collapse of Scientology, but in addition to being Keeper of the Source, Miscavige plays an odd role of also being a scapegoat for some people to blame, that Scientology isn't working for them, or that it is not clearing the planet. Where Miscavige falls short, Sea Org members feel they have to stick it out, sometimes for decades, to "do it for Ron," just as Rathbun and Rinder did.
However, if Miscavige got in a bad situation and had to retire or step down, I don't think Scientology could function by committee. It needs a dictator, someone with "command intention," a symbol of "certainty" in Ron and the "tech."
The big crack Tommy could cause in court, whether he says in his deposition that he left Scientology, or has to say what Miscavige ordered him to handle Marty, is that it will affect new membership the most. Karin Pouw does not speak in public, and the last 3 spokescreatures for the cult left Scientology (or at least the Sea Org in Tommy's case) and did just what Miscavige ordered, in spite of their high level of "self-determination." Since many scilebrities thought Tommy was such a nice kid, they will have some questions as to what happened if they find out he's left, or testified against Miscavige. If his family can't continue this dynasty of loons, who can?
Leah Remini's deposition, because of her popularity, may draw the attention to this case that does the most damage to Scientology, as more people find out about the Squirrel Busters and the way the cult treats ex-members and anyone around the ex-members.