Altru Ideas

I am setting up a new membership program for our corporate memberships and I was looking to do it on the new Contribution based option. The problem is that I want to use the program going forward, but it will drag in all the current people in our database that meet the criteria. Is there a way to either limit it so they don't get dragged in? Limiting it to organizations wouldn't necessarily work, since some of them would get dragged in because of their giving history and I don't know if limiting it to only being able to participate in one program is a solution because I can think of examples where there is some overlap. Any ideas? Thanks.