The best suggestion I can think of is to stress the size of the cult's operation. After all, they're trying to collect the biggest dragon hoard ever; it stands to reason they're not confining themselves to raiding just the area around Greenest. Treasure and cultists should be pouring into Baldur's Gate by several different routes, including the river and perhaps even by sea. Thus, there will be quite a lot of cultists in town who have never seen the PCs, and the cultists who travel with the caravan need not all be veterans of Mondath's encampment. (An added plus to this approach is that it starts to open out and reveal the epic scale of the plot.)
Right, so just because Mondath's on to them doesn't mean everyone will be. And turning Baldur's Gate into a meeting point also makes it so the cult is less likely to change the route just because some pesky adventurers are on their tail. It would be too awkward to try and change the details of an operation of that size at the last minute. One will have to assume that the cult has its fingers in the various power groups in the city, though, to help ensure that they don't get stopped there.
Are any of your PCs Harpers? A Harper contact would be a good source of information on the scale of cult activity in town.
Yes, my wife's dwarf wizard just joined the Harpers. The elf arcane trickster is still considering it. The druid joined the Emerald Enclave back in Elturel, and the human fighter is probably going to join the Lords' Alliance, once I set that up (I'm going to run another short side quest involving some corrupt Flaming Fist soldiers that will bring the PCs to Ravengard's attention).
The PCs could also be encouraged to disguise themselves so that they'll be less likely to be recognized by cultists who have seen them before.
I did have Leosin and Ontharr suggest that, but the players didn't really do anything. I think the elf changed his clothing, but that was about it. The dwarf refused to shave his beard. Besides, there's only so many ways you can disguise an 8-ft tall goliath ...
EDIT: As an aside, I'm still struggling to figure out what to do about Talis. As you may recall, one of the PCs in my game has the "Talis was a childhood friend" bond, which suggests that she might have been kidnapped by dragon cultists, and that the PC's investigation into the cult has led them to Greenest. I had originally thought about planting some clues about Talis there but I never got around to it, so it ended up being a bit of a dead-end.
Anyway, the player of the PC in question wants to visit Talis' family to let them know she's had no luck, so in trying to figure out who her family might be, I settled on Coran. He seems like quite the womanizer, and I figure he's probably left a whole string of half-elven bastards in his wake. So why not make it so Talis is Coran's lovechild? Perhaps she happened to be staying with him for a while when the PC was growing up and they got to be friends by attending all the same parties and such.
This way I can introduce Coran as a famous local person in the Gate, and have him serve as a clue dispenser and/or quest giver, as he is wont to do. The elven PC in my group is also on the hunt for an elven cleric who can heal him of a head injury, and I figure Coran might be the one to point him in the right direction for that, as well, since elves don't have a big presence in the Gate.