It really comes down to how you have set-up your code. In your particular case, there wouldn't appear to be much benefit.
But what if your code required you to have multiple instantiations of your model across many different controllers? For example, maybe you have a model to your user repository. There may be many controllers which need to get information about the user.
Then it would be a hassle to go through all your controllers changing all the references (i.e. your example 2). Much better to just change the repository once (i.e. your example 1).
There is never one size fits all in coding. The best you can do is code for what you need now, with an awareness of any potential solutions which may aid flexibility in the future. My view is that the repository pattern is one of those solutions which aids flexibility. You may never need to change the model, or move to a different database, but the effort in coding with it now is minimal compared to the hassle you will have if you ever did want to change your db.