I think you're forgetting some major parts here.

Nanamo's power is limited by the Syndicate, which is a group of the wealthiest individuals (and in Ul'dah, wealth equals power). She was essentially a puppet to them.
Said individuals also weren't too happy about Nanamo's attempts on dissolving the Syndicate, with the help of the other two city-states (Gridania and Limsa Lominsa).
Teledji was especially unhappy about this, and made an attempt to assassinate the Sultana. An attempt that Lolorito had learned of. While he wanted Nanamo to be removed from power as well (along with Raubahn), he had no interest in doing so through killing her.
Why he didn't apply the antidote sooner? Because this is Lolorito we're talking about. If he thinks he can profit off of something (in this case, holding onto the antidote), he'll do it. Lolorito isn't some goody two shoes character, he's still a Syndicate member focused on wealth (because, again, wealth equals power in Ul'dah).