I've done a little bit of crude testing. So far I've gotten this bug reliably in earth missions, and it's never happened to me in other ones that I've noticed. However, I DID see it happen to someone else's Charger in a defense mission on a later planet (I'd have to check to figure out which one, sorry), so it's clearly not that simple. It's possible that there's several different bugs that all cause the same end result, or maybe some background element of Earth missions that exacerbates it, or any number of things.
In any case, I'm not sure that Warframe supports that kind of console command. as far as I know the only commands in game are chat-related, so there may not be a system set up for that kind of command. Plus, if they make that kind of script, it's likely that they could set something up to have it run automatically if the pet is inactive for too long. Honestly, that'd be plenty enough fix for me. It would be nice for this to be completely fixed, but even just a stopgap measure would be nice for now.