The guilds weren't a big concern at start. After I've read some posts on this forum and in the middle of the campaign I destroyed some of the numerous thieves' guilds in my cities. Now I have a HQ for Thieves in Marseille (after I destroyed the one in Antioche), for Explorer in Florence and for Merchants in Constantinople.
I use alot of spies and in Constantinople I was offered a merchant's guild as soon as I destroyed the thieves one.
Now I'm trying to get the theologian HQ in Iconium so I'm planning to build all church line buildings and recruit all priests there.
It took me time to figure out I had to destroy the thieves guild to get others there