You want all removed but diplomat and merchant, eh? That is:

- spies
- assassins
- priests/imams

Spies are entirely uninvolved in game mechanics except against each other, so simply removing them should work.

Assassins are similar, but also involved in some mission types. So in addition to removing them, you'll have to go clean out whatever missions they are required for to make sure you don't pop missions that cannot be accomplished. Not sure what file that's in (assuming it's in one we can access).

Priests and imams will be hard work to remove. They spread religion, and religion is tied to unrest. So to remove them, you need something that pretty much instantly converts populations to a new religion when they're conquered by a different religion, otherwise it will probably be too difficult to control conquered populations as churches alone have trouble converting entire populations. My idea is this:

Set all city and castle walls to give some insane bonus to conversion percentage. This would be in the export_descr_buildings.txt file, and the first 2 things in it are all the city and castle walls. If you need help with the religion conversion bonus, look in the file for the church buildings that already do this, it should be easy to figure out. This way whoever owns the city immediately gets the insane bonus for their religion in the region, which should convert it VERY fast and eliminate the need for priests.

Of course you could just remove priests from the game and deal with having religion only controlled by churches, but it will probably tend to make the church buildings WAY too important in the build order, which is why I suggested just making religion inconsequential.

You'll also have to be sure to remove heretics and witches, as without priests or assassins there will be absolutely no way to deal with them.

...and remove the pope-inspired missions that ask you to recruit priests. Yeah. Lots of work.

And I still forgot some. What the heck are you going to do about the papacy without cardinals to get elected into the college of cardinals and become popes? I don't think we can actually remove that from the game, and I honestly don't know what the game does if there are no cardinals and no pope. Could be a real mess...