Sure.
Just do it all exclusively outside of the game.
Help me, i'm lost
^ what Vucar said would be the easiest method. Use forums/discord to communicate, use dead drops to deliver proof of assassination/pay etc. Like the Dark Brotherhood in Oblivion.
If you're a roleplaying assassin guild and don't want to use third person, then again I would reference Oblivion and have a 'Listener' type character, make them the only person in the guild to know everyone's identity and they can arrange things, without any other members knowing who's who.
I believe there won't be such things a assassins guild, will most probably only be groups of people with no actual guild game mechs, well unless you are in an evil place cause what makes you a guild is registering to the count or local aristocrat (can't remember wich), and registering your thief/assassin/deviant guild to the authorities is quite dumb hahahaha. my best advice to you if you want to hide your guild is to not be registered as a guild just act as a group of people and use normal houses as your bases maybe dig a hiden dungeon but do not register it as ''guildhall of the baddies'' :P