While i agree wit some people here, that the current system makes sense from a real life perspective, i have to agree with OP, when he says that is a fun killer, especially given the current state of diplomacy and the strategic AI.
If you want to play as merchant/artisan right now you can go 2 paths. Either you do solely that and never swear allegiance or found a kingdom yourself. I would not know why anyone would choose to do so, given that trading and passive income from caravans/workshops is just monotone, but if others enjoy that, so be it. In this case there is no problem, since you will never be at war with anyone.
Other way is, to start of as merchant/artisan and use it as springboard to facilitate your political growth. In that case you have decide from the get go which faction you want to join and thus be able to plan your workshop locations. Even then, since war declaration is all over the place right now, you wll still loose some workshops, because some idiot lord decided to raid some village or caravan of a country on the other side of the map. And this is just frustrating.
Thats why i would support a change in this mechanic. Having them not produce income while at war, having them operate in secret, but at a reduced profit, paying some compensation for a complete loss or maybe make it an actual decision to be taken by the lord/player.
There could be laws regulating workshops, the decision to revoke workshops could be a concious decision and not just automatically, because you are at war now. Maybe if the lord i am at war with now really likes me and/or has some traits like geneous or honorable he might just leave my workshop as it is. If he hates me or has traits like calculating, he might just take it. There could be done much more than what we have now and anything is better than what we have right now.
I dont midn if there are risks, on the contrary, there should be risks to such any easy moneymaker. But the risks have to be calculateable and the possibility for planning by the player has to exist, so it feels good. Being forced to plan out your playthrough fromt he get go, so you do not waste hours of playtime by mid game, is not an optimal solution. Even more so when even then you can not avoid it, because of stupid AI.