I started using the Custom Launcher some months ago, after using this method for a long time. The launcher creates .package files up to 1 GB in size, and then makes new ones as needed. I'm currently at 4 files (yeah, I go a bit CC crazy) but there's barely any performance hit.

One thing to watch out for is that it actually keeps a backup of every file added, so twice the disk space is used. If you have disk space troubles, it might not be the best option. Otherwise, it works great.

I just tried removing the lot, and it seems to have worked. I placed a new one on the same spot (maybe not exactly the same, it's a bit further from the road than it was, but it's the same area) and now the zergswarm stopped.
Just to be clear, it's necessary to remove the whole lot, even the empty square. Then a new one can be placed. If the lot in question isn't present in the list of pre-made ones, back it up before obviously.

Of course this isn't a true solution, just cures the effects. The Rapture Effect might just come back at any time.

I'm suffering from this bug too in one of my saves. The townies just SWARM to the film studio, and stand there. Like they're waiting for the Rapture or something.
My pc is kinda average, enough to not have them "crucified", but they just stand there. At best, some take photos of the celebrities.

Resetworld and resetsim * clear the place out, but it fills up soon after.
From the map view they can be seen just swarming like zergling to the place, it's kinda funny to watch but still, it tends to clog up the game and if I don't step in, they just let themselves die.
I'm tempted to just destroyallhumans, but I'd like to avoid that for now if another solution is possible. Especially since I believe it will just happen all over again.

The baked good table doesn't seem to work. Even with the price set to 1, people show up, get to the table, then leave without ever buying anything.

Plus a couple of bugs I experienced days ago (not the latest AM, so they're probably fixed, but I don't think they've been reported).

1) At Medicine career level 10, endless sims were spawned, all at the same position (World Renown Surgeon). Kinda funny seeing a huge crowd of doctors trying to get into the hospital, but they cluttered the town, until I therapture'd them away (sim count was at 610).

2) At some point the game would hang every time at 5.59 (like the old 1AM hanging), until I figured out it was due to the alarm clock (the old one). Even on a new save, setting the alarm on it would hang the game.
I haven't tried using it again, and the digital one works fine.