You're definitely not wrong that it's not guaranteed she would win. She'd probably have had a better chance though. It would've been harder for Trump to make his pitch in the areas Clinton did well in.
There is no way to predict what would have happened. National popular vote would completely change both campaign strategy and voter incentives, and the results were already so close that as much as casting ballots on a Sunday instead of a Tuesday might have been enough to change both the popular vote and the electoral college result.