I'd suggest reconsidering the idea of one site per subject before ruling it
out. That's probably the most viable route to using OpenClinica for this
use case with minimal customisations, since sites and studies are the only
built in mechanisms for restricting interactive access to subject data
(besides Participate, but that's a separate app).
The software you might need to work on then is a tool to automate the task
of creating one site per participant user account. This could be something
that works directly with the database, or something that automates
interaction with the web app via a browser (selenium).
For non-password authentication, there is LDAP but it won't save any effort
if the LDAP account isn't used for anything else. Many months ago there was
a pull request / contribution on GitHub which implemented SAML
authentication. It wasn't merged, but you might find a use for it.
It looks like delegated authentication is on the horizon for OpenClinica 4
anyway. Either you could trawl through Jira and GitHub for clues, or maybe
Krikor will talk about it at the next API design advisory meeting (not sure
when that is).
Lastly, this kind of thing may be suited to RedCap. It's designed for
longitudinal surveys, completed either by staff or participants. I haven't
watched it too closely but it may be at or approaching the point where it's
usable as a clinical research EDC.