You can prevent each level's code from running at all if you write 0x90 (5 bytes) to the addresses below. This will work regardless of mod order.

Station Square 0x4231E6
Egg Carrier Exterior 0x4232C9
Egg Carrier Interior 0x4233BB
Mystic Ruins 0x4234AD
Mystic Ruins Past 0x423554
Hedgehog Hammer 0x422B2A
Emerald Coast 0x422B68
Windy Valley 0x422BD3
Twinkle Park 0x422C3E
Speed Highway 0x422CA9
Red Mountain 0x422D14
Sky Deck 0x422D84
Lost World 0x422DEF
Ice Cap 0x422E5A
Casinopolis 0x422EE8
Final Egg 0x422F71
Hot Shelter 0x422FFF
Chaos 0 0x423088
Chaos 2 0x4230B7
Chaos 4 0x4230CD
Chaos 6 0x4230E3
Perfect Chaos 0x423108
Egg Hornet 0x423146
Egg Walker 0x42315F
Egg Viper 0x423178
ZERO 0x423196
E-101 Beta 0x4231AF
E-101 MK2 0x4231CD
Sky Chase 0x4236B1 and 0x4236E0
Sand Hill 0x42370F
Twinkle Circuit 0x4235EC
Chao Gardens and Chao Race 0x423795

Note that PVM, SET and other file replacements are currently still executed at mod startup, so you may need to replace files with the _DC suffix in addition to ordinary SADX files in your mod (e.g. replace SET0100S_DC.BIN in addition to SET0100S.BIN).