The authors intention of wiping the repository is in direct conflict with one of the demands (the last bullet):
"Immediately take steps to preserve all documents,
tangible things and electronically-stored information
potentially relevant to the issues addressed in this letter."
I'm not a lawyer and don't know how enforceable it is, and I doubt that WhatsApp would take any action once the repository is no longer a concern, but I'm curious if there are any comments about this.
"I find your comments offensive and in violation of the Bullshit Act 2012, and hereby request that you delete your comment and jump off the roof."
IANAL, but unless it's a court or other public body telling you to do something, you are under no obligation to do anything whatsoever. Lawyers use scary words to intimidate and scary regular people but until the courts are involved, they're just posturing. In doubt, always ask a real lawyer before doing anything rash.
However, even if they did keep the source code, there are issues and other information on github that would not be preserved. I think it's safe to assume this information is very relevant to litigation involving a scenario such as this one.
Even if that wasn't a factor, the court may get the idea that the repository was wiped in order to destroy evidence. Convincing them otherwise may be technically challenging.
Self-incrimination does not apply in civil cases. This is actually a pretty standard warning against spoilation of evidence in a potential civil case -- if a party doesn't convey such a warning, then, in the event of ensuing litigation, the court is likely to find that they did not trigger a duty to preserve evidence on the part of the defendant.
If a defendant is so warned and destroys evidence, then the trial court may impose sanctions such as an adverse inference instruction (essentially, instructions to the jury that any evidence not produced by a side should be inferred to be damaging to that side's case). So any lawyer who stayed awake during civil procedure is going to make sure that they keep that option alive in the event they decide to sue.