"Civilian structures are being left alone for now".
Two things in the statement that I find interresting:
1) structures: Surely civilian ships tried to flee. If they were left alone, the general would habe mentioned it, and not only said structures.
For me that sounds like the minbari jump in, blast everything in orbit (no matter if military or civilian), make some quick strikes at the surface to take out military bases and move on to the next system.
2) for now: As I said, neutralize a potential threats and move on to the next one without wasting time with helpless civilians. Those can be dealt with at their leisure once the military is gone.
Wiping out the complete population of a whole planet takes time after all, even with the minbaris technology. And it leaves you open for attacks from behind, unless you guard your back, in which case the "pacification" takes even longer.
And in the Minbari Civil war they showed that they have little to no scuples to commit genocide if it is "justified" or "for the greater good".
You are right of course that it is a theory. Since the war never progressed to the point were the absolute truth would have been shown, speculating is all we can do (or ask JMS).
But from all the information we have about the war and the Minbari mindset, I think it's the most likely outcome that the Minbari would have wiped out Humanity, or at the very least destroyed Earth.
With the Minbari way of twisting words around "follow them to their homeplanet and kill them all" could be constructed as only killing those on that planet.