I'm not sure what I'm supposed to do. I just bought the game an extra time for a family member through steam, tried to log into my account through the same steam launcher, and it worked fine this morning. Now that I try to log in it tells me that my subscribed account that is 4 or so years old is not a registered service account. I just bought a subscription on that account as well, and now it's pretty much wasting away with the money used for it. :s
Sounds like you'll need to contact SE (these forums are more for players to help other players), but have you tried logging into the Mogstation which controls all the XIV related account settings? That should give you more information as to what is going on.
But no I can confirm they don't revoke service for logging into the Steam version from non-Steam, because they're actually exactly the same download (all updates comes from Square Enix directly, not Steam. The only actual difference is the code used to activate flags the account as Steam so all expansions must have a matching code).
Only thing I can think of is, do you not have a one-time password token by chance? I have one, so never witnessed this issue personally, but I seem to remember players without them experiencing temporary suspensions after logging into their account from unexpected IP's. If I'm right it's just until you contact them and is a precaution against getting hacked, or something... I don't know for sure. Software token is free though, last I checked.
Like someone else said, you could try logging into your account at mogstation and that should tell you the status of the account.
I would imagine they wouldn't even let you log in through steam since you didn't have a steam key since they seem to treat it as different platform such as PS3/PS4. Have you tried logging in through your non-steam client?