Yep, pretty much. I've only ever dealt with low-load applications so there was no load balancer. You just put the Lisp server in a state where it refuses new connections (serves up a "temporarily down for mx" page, or reconfigure the ngingx front end to do that), wait for existing connections to finish, and then restart. It's no different from any other server.
e.g. remove from load balancer, wait up to n minutes for connections to drain?, git pull, quit, restart Lisp, re-add to load balancer. ?