Nope you cant have a rat assasssin who is "good"
Ill explain a bit.
Your start in either qeynos or freeport dependant of if you good or evil. If you are neutral ie humans, you choose a city. Once you have done that you either follow the path of good or evil. A good person would not be allowed to move freely in freeport and vice versa. It has been stated that you cant enter those citys at all although you might be able to enter an opposite aligned guildhall for a guild you belong to via the sewers.
The archetypes of fighter, mage, priest and scout have trainers in each city, as do the proffessions that you specialise from these, ie Warrior, Brawler, crusader, Sorcerer, Enchanter, Summoner, Cleric, Druid, Shaman, Rogue, Bard and Predator.
At level 20 you choose a final class. You want to choose Assasin, this is an evil class and only trained at Freeport.
BUT
You can only swap sides once, to do this you need to do the betrayal quest and this has to be done BEFORE level 20. So its imposible to be a good aligned Ratonga Assasin. You would become good before you could become an assasin. You would still be a predator when you switched giving you only one option and that is to become a Ranger.
Its like this so you cant cripple yourself by never being able to take a class where conflict could occur, ie good Shadow Knights, Evil paladins etc
1/3 the classes are defined as good (ie paladin), 1/3 are evil (assassin) and 1/3 are available to both ie guardians or and of the druidic based classes (fury or warden)
Like players all guilds have a home city that they work for and assist. That aside there is no reason for you not to play a ratonga assassin and belong to a guild based in Qeynos. YOu could help that guild and would not suffer negative faction. There are not unlike WOW any barriers to prevent you from grouping with "good" aligned players. Where you would loose out is that the guild would get quests from Qyenos that would improve that guilds standing in that city, and while you could help in those quests you would never benefit from the rewards the "good" aligned players would get (respect, items etc), also visiting the guild hall if they had one would be very difficult current concepts are you sneak in via the sewers so you never see the city and could never enter it, all you could enter is the hall itself.
There is provision for a type of guild that does not seek to take part in the quests and prestige progression, this are still aligned to a city and all the travel issues still remain but no one gets any benefits as they cant do the quests. THese are called families i think and basically just provide a communication channel.
Sorry for the waffle.