You are "allowed" to join an NPC sorority, even if you have been a member of a local sorority. That being said, you need to let the women in the sorority you are interested in joining know that you were in a local sorority, because it might impact whether or not they give you a bid. I know that it's probably tempting to just not mention it, but think about how your future sisters would feel if they felt like you withheld information to try to look better to them. Also, you might feel like you cheated your way in, which could tarnish your feelings about the NPC group. It is better to be upfront about it, even if you think that it might diminish your chances of getting a bid.
As for disaffiliating with your local, I'm no NPC Green Book expert, but I don't think it's necessary, just to join an NPC sorority. I would suggest that, if you do receive a bid from the new group, that you talk to their Panhellenic advisor about it. That is, unless you just want to go ahead and disaffiliate now because of the problems that you mentioned in your post.
Good luck!
ETA: I just re-read your comment about it being explained to you as a community service sorority recognized in the community. I'm not sure that would pose a problem at all with the NPC group. They might look at it as a plus that you were involved in something like that. My sorority had many members who were also involved in those types of organizations.