Titania only had one Pokemon in the sewers that wasn't far above the level cap, so it actually would've been reasonably possible for the player to defeat/stop her. But that would mean you'd be on your own in the double battles, and navigating the sewers would probably be a lot more difficult/Titania would be willing to leave you behind. It's not something you really could've afforded to do.
I actually don't think Saphira was in the wrong. Titania was, but I can't really blame her after Amaria jumped down the waterfall and got captured, then having to spend so long down in the sewers and being on edge from fatigue and hunger. It's just unfortunate the ones who got in her way were the least violent members.