It was mentionned Legion soldiers are more loyal to their commander than to their Emperor.
They only kept fighting with Eorzean alliance thinking Nael was still alive and following his order till the end.
So, I don't think Nael's troops will swear allegiance to a new leader, the 7th Legion may be disbanded entirely.

A community manager also wrote that the japanese version of FFXIV didn't use the word "legatus" or "legion", it's only the result of the english adaptation. I think the german word was different too. It's probably better not to think over the accuracy of the Legatus system.