At this point in time, OP can take down the repo (but not the 115-and-counting forks thereof), or modify it (someone suggested removing keys issued by Snapchat), or not. How will this set of options change if Snapchat file suit? Of course one must respond to a suit, but couldn't one's response be "ok we've complied with all requests"?
If you're telling me that the suit could allege OP owes Snapchat money for his/her misdeeds, that's true, but it's always true, even after one complies with the sort of namby-pamby "C&D" we see here.
Without specific answers to many of the foregoing questions, this message amounts to asking OP to forego all use and value of work that OP has personally performed, merely on Snapchat's say-so. So, actual meritorious C&D's require some actual work on the part of the sender. This letter took some knucklehead five minutes, so that's about what it's worth.
C&D's are usually courtesies to avoid...
...the expense of an actual lawsuit. In many cases a vague and overbroad (see above) message is mere bullying, attempting to imply threats that would be impossible to articulate or enforce. Papers filed in a court are held to a higher standard, and penalties are enforced. The fact that OP might be well-advised to retain counsel in response to this turd is an indictment of the USA legal system.
A lawyer can analyze the facts of what you have done, and provide you with advice as to whether it is likely to be found to be an anti-circumvention device under the cited section of the DMCA and, if so, what the likely consequences of that are and what steps you can take to mitigate any exposure you might have in that regard (including, if there are any, steps short of taking down the existing offering.)
Of course, you could wait to see if they actually file a suit rather than having a lawyer look at the C&D, but if you do that, then there will be less, not more, that a lawyer can do for you.