I generally exclude my traps from the civilian alert burrow. If I then close the outer drawbridge on one of the entrances I temporarily extend the burrow to cover the cage traps so the captives can be hauled off and the traps reloaded. That burrow part is then repainted to remove the area again afterwards, and the drawbridge is opened again for a new batch (Typically I've then closed off another entrance, extended the burrow in that direction....).
Otherwise, cleaning is a job, but I wouldn't recommend manually disabling it on each dorf to later enabling it again.
Goblin assassins sounds interesting. The closest thing I've got is one or two baby snatchers.
I haven't seen much of the invader pathing bug in 0.40.X, so most of my fortresses have had their share of sieges (see Location, Location, Location... above).
It may be that mostly using pocket worlds helps, but the 0.42.X flipside is that I've so far have had a total of 1 visitor over half a dozen packet world fortresses (the larger worlds have successfully provided visitors). My current fortress is an exception, though. I've only had hello/good by goblin sieges (plus two black towers' worth of undead), and then the goblin civs have imploded, with 2 goblin civs that are considered non failed, but those contain 0 goblins and something like 1 and 4 others. The world, however, contains 16000 goblin outcasts and 10000 regular goblins living in sites not owned by any civ. The goblins who did pass my way came from a civ that lost its only site (to another goblin civ) 2 years after my fortress was founded, but kept up their cameo visits for another 5 years.