You have to use callback in this case. E.g. Define you function in your JavaScript code as:
function alertRedirect(message, url) {
new Messi(message, {title: 'Warning',
modal: true,
buttons: [{id: 0, label: 'OK', val: 'OK'}],
callback: function() {
location.href = url;
}});
}
And call it in your .net Code:
ScriptManager.RegisterStartupScript(this, this.GetType(), Guid.NewGuid().ToString(), "alertRedirect('this is a message','Register.aspx');", true);