try this:
container.Register(
Component.For<ISessionFactory>()
.UsingFactoryMethod(() => GetSessionFactory("1"))
.Named("1"),
Component.For<ISessionFactory>()
.UsingFactoryMethod(() => GetSessionFactory("2"))
.Named("2"),
Component.For<IRepository>()
.ImplementedBy<Repository>()
.DependsOn(Dependency.OnComponent(typeof(ISessionFactory),"1")),
Component.For<IReadOnlyRepository>()
.ImplementedBy<ReadOnlyRepository>()
.DependsOn(Dependency.OnComponent(typeof(ISessionFactory), "2")));