Is there any reason troops refuse to follow a LD?

[Chazar]

Cainehill said:
Hmm. That'd give a new way to poison mercenary troops though - add something to the merc troop with a disease / cold / poison aura, so that it kills the merc troop _and_ potentially the new paymaster's troops.

No, for your own troops do not carry the mercenary tag and thus return to the current province's garrision if the mercenary commander returns (like for any other vanishing commander (personal teleport, wind ride, assassinations,...)!

So there is nothing new that you could not already do in terms of nastiness. Of course, you can already use another commander and place disease spreading creatures next to them on the battlefield, as Wish_For_Blood_Slaves already pointed out.