Should I discourage using messaging apps for research group communication?
No. If you are worried about your colleagues being able to delete the messages from Facebook / Whatsapp, how do you cope with them calling each other? Or worse: actually talking, walking to their office and just copying files? 

I'm all in favor of making communication easier, as insufficient communication between researchers is wasting millions of hours every year. But it should be with the goal of facilitating communication, you'll never get an environment that's completely traceable. That a wiki will have some kind of versioning or history will be an additional benefit, not a reason to use a wiki. 

And besides, who's going to check all that communication? Scientific literature is full of fraud and misconduct that's in plain sight and not corrected. Errors in literature are there because people do not care and have no time, not because they lack the forensic tools.