This whole guild thing wrt Merchants Guilds is odd...

In my Scottish camp, I conquered France, and in a time honored tradition, destroyed all of my enemy's buildings and ran off. Money boost, then go on to fight elsewhere. Anywho, nearly every city had a Thieves Guild, and after I took those out, the next turn (amidst the riots) was the Merchants Guild trying to set up shop. Course, that may be due to the fact that I have the Merchants Guild HQ in Edinburgh, even though I never built one Merchant from there.

*shrugs*