Depois de refletir sobre a resposta do jd, consegui obter o mesmo resultado para o framework postgresql 9.2, sqlalchemy 0.8 e flask 0.9:
from sqlalchemy import event
from sqlalchemy.pool import Pool
@event.listens_for(Pool, 'checkout')
def on_pool_checkout(dbapi_conn, connection_rec, connection_proxy):
tenant_id = session.get('tenant_id')
cursor = dbapi_conn.cursor()
if tenant_id is None:
cursor.execute("SET search_path TO public, shared;")
else:
cursor.execute("SET search_path TO t" + str(tenant_id) + ", shared;")
dbapi_conn.commit()
cursor.close()
