Well.. the point in the whole matter is this: If a terrible fate befalls the shopkeeper, the game will ensure that they have a chance for comeuppance with the- Shopkeeper guarding the next level's exit- game mechanic. And it IS a game breaking mechanic because it destroys the risk-reward aspect of an important fork in the game's road- Will you choose the path of the thief and risk the retribution of the many angry shopkeepers that will follow, or will you choose the path of the consumer and deal with the dungeon while worrying whether you have enough gold to afford an ankh and a cape by the time you find the Black Market (safely, mind you).
I would first like to thank you for the time and thought you put into this. It's very rare I find something more then a paragraph long worth reading let alone read it multiple times. I guess when you put it that way does make it sound like a cheat if you know how to do it without luck involved. Maybe as a counter balance, all shops in world 1 get declared unsafe and are no longer manned or stocked.
On a different take, there are MANY opportunities for an Idol boulder to roll into a shop in Area 1, and because Area 2 shops are far rarer to spawn, they are the prime and few opportunities to stock up before you reach the point of no return in equipment. Because of the layout of the initial area, the top 12 quadrants of space are fair game for a Golden idol (and thus a boulder) spawn. That said, the shops can spawn in any quadrant not occupied by an entrance or an exit, or somehow impeding the ability to enter the exit. Probability is fair that you'll come across an idol that is on the same X axis as a shop, or located above a shop and whose course could be manipulated in such a way that it would descend to the next level where the shop may have spawned. You're essentially playing a game of luck involving randomly generated rooms as to whether your spelunking experience will be a breeze, or be somehow derailed by either scenario (Thief or Law-abider) as the game stands.
I see your point, but the same thing could be said of getting a Jetpack, climbing gloves or cape in a crate in the first level.
Finally- if the other two points don't faze you, consider this. How would you approach this addition from a game-engine standpoint? (If Trigger: Boulder, Shop on same X axis, Shopkeeper Panick) okay.. so what about if the procedurally generated rooms throw you a curveball? You trigger the boulder and climb a rope facing a level wall, the boulder slams in and gets stuck. SOMEHOW, all the way across the map, the bearded bastard gets spooked. No. Of course not. He knew the dangers of being in a dungeon full of indiana jones wannabes and he packed and trained accordingly (Air Jordans that let him jump higher than the crappy spring shoes he sells and a fully loaded shotgun). Ignoring that, the game engine doesn't even REGISTER physics unless they are within a visible (and slightly beyond visible) range of the player. (set a bomb and run off 2 screens away to test this, come back after the explosion's sound and the ground will be perfectly untouched).
Um... yeah, about that bomb physics test...I feel I should point out that I have east Asian language support on my system. I don't know if that would effect Game Maker software but I have seen it effect other things.
The shopkeeper can't even run if you aren't within that predetermined distance from the shop. How would you suggest that the shopkeeper escape the oncoming boulder if the game doesn't allow him a point of descent. Does he just Plot-teleport away?
If he's not one screen, why not? Though if this does happen then most if his stock should also plot-teleport away. See, more balance right there.
The idea is flawed on multiple levels, and it's hard to think that it is capable of being added without buggy functionality due to the chaotic nature of the way the game generates rooms.

Considering my only programming knowledge is forgotten by now must likely I have no rebuttal for this. One thing I do request that you remember is that my suggestions are for version 1.X, not 1.0. And even then I know they are just suggestions.
Speaking of suggestions, how about a lawyer who appears between levels like the tunnel man who for $100,000 will get your criminal status cleared?