sorry for delay, swamped with reviews and stuff.
One thing that worries me more than others is that you introduced circular dependency between ap_association and l1dbproto. ap_association needs to depend on l1dbproto of course, but opposite dependency should be avoided. I see that you imported lsst.ap.association into ap_proto and create_l1_schema. I guess you will be needing a script to create schema for ap_association, and I think the easiest is to just copy create_l1_schema from l1dbproto and modify it for your needs. ap_proto does not really need to use exactly the same schema as ap_association so we can probably keep whatever schema it was using before (and I can update that later to match ap_association if needed).
Another thing that I want to check before approving those changes is to verify that degrees to radians conversion works as expected. There may be other locations in ap_proto that depend on units of ra/decl columns, the code may still "work" with different units but it may produce wrong results. Give me day or two to try to run stuff from your branch and see how it behaves.
[Also, if you are ready for merging can you open pull request on github so that we can comment on the code? -- taking this out, took me too long to write my comment]