I just keep making them so I get the guild HQ's, if they die/get taken over it's an excuse to make another one. Merchants/Assassins that have no guild training are almost useless. You''ll be wasting a bunch of turns blowing up churches and other things before you can even think about actually assassinating anybody. A 1 star merchant holds up a big flashing "seize my assets" sign where ever he goes. If it's your only option make sure he's somewhere in your own land with a watchtower looking over him so you can move him off a resource whenever another merchant gets close.

On the other hand if you have a guild HQ and are popping out 4-5 star merchants/assassins you can come out with a good chance of being able to kill rebels or at least just spending a few turns sabotaging to get a 7 skill assassin. For merchant's any new one will have a 95% shot at taking over any 1 star merchants that meander by and will be skilled enough to risk sending away. I love guild HQ's, I have a theologians guild HQ with a huge cathedral and it popped out a 25 yo bishop with full piety.