So the IBM Deployment Engine (aka ACSI, or Autonomic Computing Solution Installer is what I believe the acronym stands for) is a really nice product and works very well if you read the documentation and warnings. As luck would have it, I forgot to read some of the documentation and warnings, so I was able to learn some things.
The OMNIbus documentation states that if you use the DE as a regular user, then as root, that all installs from that point forward will only use the DE instance that was installed by root (the global instance). It also states that if you uninstall the global/common instance, then the DE is uninstalled everywhere.
The situation that brought me to this point is that I installed TBSM 6.1 on Linux as the user 'netcool' (so it uses a user-specific DE). I then tried to install CCMDB 7.2.1 on the same machine as the user 'root'. This failed early in the process, but not before a new global/common DE was installed. I gave up my CCMDB install dreams and proceeded to install an OMNIbus probe as the user 'netcool'. This gave me an error that I was currently using the global DE on an installation that had been performed using my user-specific DE and I should abort the installation. After reading the above OMNIbus documentation, I didn't want to uninstall the global DE (for fear that it would wipe out everything and I wouldn't be able to upgrade any products). However, since I had a copy of my VM, I gave it a shot. What I did was:
./si_inst -r -f
This scared me a bit because it did COMPLETELY remove the /usr/ibm/common/acsi directory and killed all of the acsi processes ('ps -ef | grep acsi' showed nothing at this point). But my ~netcool/.acsi_* directories were still there (I don't know why, but I have two of these directories - ~/.acsi_netcool and ~/.acsi_myserverhostname). At this point, I re-ran the probe installation as user netcool (nco_install_integration), and I got no error messages, and the install information was added correctly to my local DE instance.
And the lesson I learned is that once you install any DE-based product on a machine as a non-root user, all of your subsequent DE-based installs need to be done as non-root users (it doesn't need to be the same user for different products, but you don't want to install anything DE-based as root).