You could add a class to the ckeditor ‘ckescroll’ (in the Appearance tab) and in your theme files add something like this (change the 200px limit to whatever you need):
.ckescroll {
max-height: 200px;
overflow: auto;
}
You can also add the two lines between curly braces to the Style input in the same Appearance tab, but that’s against best practices and frowned upon.