Ok, so if I move the logic around I no longer have any reference to a ViewModel in the UserRepository. I now have a method in the UserEditViewModel to perform the updates. My HttpPost Edit ActionResult in the UserController has also been updated. Does this seem acceptable?

//In UserEditViewModel I have this new method

public User UpdateDomainModelUser(User user, IEnumerable<Role> roles)
{
    user.UserName = this.UserName;
    user.Email = this.Email;
    user.FirstName = this.FirstName;
    user.LastName = this.LastName;
    user.PhoneExtension = this.PhoneExtension;
    user.IsApproved = this.IsApproved;

    foreach (RoleViewModel rvm in this.RoleViewModels)
    {
        if (rvm.Checked)
        {
            //add role if it doesn't exist
            var roleToAdd = (from role in roles
                                where role.RoleId.Equals(rvm.Id)
                                select role).First();

            if (roleToAdd != null)
                user.Roles.Add(roleToAdd);
        }
        else
        {
            //remove role
            var roleToRemove = from role in roles
                        where role.RoleId.Equals(rvm.Id)
                        select role;

            if (roleToRemove.Count() == 1)
                user.Roles.Remove(roleToRemove.ElementAt(0));
        }
    }

    return user;
}

//And here is the updated UserController ActionResult

[HttpPost]
public ActionResult Edit(UserEditViewModel userEditViewModel)
{
    if (ModelState.IsValid)
    {
        User user = unitOfWork.UserRepository.GetUserByID(userEditViewModel.UserId);
        userEditViewModel.UpdateDomainModelUser(user, unitOfWork.RoleRepository.GetRoles());
        unitOfWork.Save();
        return RedirectToAction("Index");
    }
    return View(unitOfWork.UserRepository.GetUserByID(userEditViewModel.UserId));
}