You can use SetProperties() on you configuration object at runtime, and then create a SessionFactory from that configuration. SetProperties takes a Dictionary as a parameter. The new SessionFactory will then use the new configuration settings.
IDictionary<string, string> props = new Dictionary<string, string>();
props["show_sql"] = "true";
Configuration config = new NHibernate.Cfg.Configuration();
config.SetProperties(props);
config.Configure();
config.AddAssembly(typeof(User).Assembly);
ISessionFactory factory = config.BuildSessionFactory();
For more info, check out this section of the docs:
ISessionFactory Configuration
Hope it helps.
/Erik