I think User Points Contributed modules is a possible alternative to consider. I. e. submodule userpoints_retroactive. Excerpt from that project page:
Award users points for their nodes, comments and votes that they have created so far, before userpoints was enabled on the site.
However, the port of this module to D7 still needs work. Maybe you can/want to somehow contriute to the finishing touch of that issue?
Another approach to consider: create a rule with specs like so:
- Event = a user logging in
- Condition like "if user points is 0"
- Action to set the initial number of user points.
Haven't actually created such rule (yet), but pretty sure that's fairly easy to do.
PS: there is also Berdir's Api documentation about this submodule ... (maybe that helps somehow).