You're right in that the issue with the Log Reader Agent will prevent the clear down of the TxLog. Howver, you've reinitialised the subscription and generated a new snapshot, meaning you don't need to replicate those older transactions from the log file anymore. This should mean you ought to be able to perform a log backup after you've done you're re-initialisation and the old log entries should be removed (I say should - there's never any guarantee with these things!).
I appreciate that time was against you on this occassion, and in that respect I think what you did was probably correct. I would just err on the side of caution as there may be others who read your article and if they don't have sufficient knowledge could land themselves in a bit of deep water because of some of the consequences. That why I've said it would have been nice to have mentioned something in the article about alerts and having the time to troubleshoot the Log Reader, and also mention about the consequences of running TRUNCATE_ONLY with the log backup.
Don't get me wrong, I'm not having a dig at you and what you're written. It takes a brave professional to write something and post on SSC with the eyes of many experts (and I am certainly not claiming to be one!) scrutinising your work. So in that respect, well done! 🙂