After a lot of searching, I finally found it:  The mythical populous patch.
It seems to work on my 3000 now, under 2.04.  From the readme:

Fixpop will modify "populous.prg" so that it will work on a 68010.
It may still not work on a 68020 or 68030 unless the instruction cache
is disabled.
 
It also modifies "populous" so that it can be run from someplace besides
the root directory of your boot disk.
 
I left some of the copy protection in, so the original disk will be
required to be in one of your floppy drives when playing the game.
 
Note that if your versions of the programs are not the same as my versions
of the programs, they have at least a 99.99% chance of not working after
this. Note also that fixpop does not do any error checking of any kind.
 
DO NOT DO THIS TO YOUR ORIGINAL DISK!!!!
 
How to use it:
	Format a blank disk.
	Copy all the files from the populous disk to the blank disk.
	remove the populous disk from the machine.
	cd to the new disk.
	fixpop
	(wait for a while)
	install it on a hard drive (optional)
	try it
 
If you run it off a hard drive, be sure that the workbench screen can be
closed, otherwise workbench still receives mouse events and acts accordingly.

 PERMSSN    UID  GID    PACKED    SIZE  RATIO     CRC       STAMP          NAME
---------- ----------- ------- ------- ------ ---------- ------------ -------------
-rwxrwxrwx 15899/4000     4001    7416  54.0% -lh5- 1c94 Aug 15  1989 fixpop
-rwxrwxrwx 15899/4000      573    1055  54.3% -lh5- 46ea Aug 15  1989 readme
---------- ----------- ------- ------- ------ ---------- ------------ -------------
 Total         2 files    4574    8471  54.0%            Aug 15  1992