Ooof. Ok so you are a Necro that accidentally betrayed and you want to go /back/ to Freeport, correct? Ok. To get back into good graces with Freeport you essentially need to follow the quest line as if you had betrayed from Qeynos originally.
You need to speak with Gol M`Tun in Antonica. To get there travel West from Haven. The beach and docks to Thundering Steppes is in the south-west area of Nektulos. Just be careful to avoid aggro. Alternatively you can exit Haven into the Thundering Steppes directly, but it drops you in the far corner of the zone...running to the Nek docks then across to Antonica is probably faster. Once you zone into Antonica run down the path and take the Griffon tower there to Qeynos Gate. You will find Gol M`Tun (the Freeport faction quest giver) hanging out near the North Qeynos gate. Do a '/waypoint -30, -14, -55' to find him.
Once you find Gol begin his series of faction quests. Take care to avoid guards and be ready for a lot of work to get your faction with Freeport back up to where it needs to be. The bright side is that you will get a good amount of AA and adventure exp doing all the bunches of quests you'll have to do. You can use my Qeynos Betrayal Guide at http://mediocrity.hoodbridge.com/timetobebad/ as a reference. It will tell you most everything that you need to get your faction up and what to do beyond that.
Good luck. Let us know if you have any more specific questions.
And for pete's sake, if you talk to a quest giver and they start telling you that you should do things to sabotage and undermine Freeport...DON'T LISTEN TO THEM. ;)