I have killed the 2 assasins took there loot and proof now i need to go to the palace but i only can take 1 route but then i get arrested by the flaming fist how do i pass them?

Very carefully.
You are suppossed to avoid them, or fight them, or just runaway. Avoiding is the best option.

A good way to avoid killing, therefore losing some massive rep, would be the sleep spell, make sure to turn off your party AI as well.

leave the area and re-enter from the southern/central part of town - you'll end up nearer the castle and not have to go through the FF patrol zone (if you've already upset them they might run after you anyway - in which case, use sleep as above or just run - they won't do much damage.

Use a scout to find a route to avoid the Flaming Fist.

thanks all for the replies i have finaly finished the game after having it a lot of years i can finaly start 2 :)
Too bad its only 1 lvl diffrence then starting a new char.