It's not really Puerto Rico's decision, of course; the referendum is non-binding. It's Congress's decision, in the end, though officially adding Puerto Rico as a state against the wishes of a _majority_ of its citizens would be quite the odd thing to do, hence the referenda to see where things stand.
> 52% is nowhere near large enough majority for a decision that can never be reverted under any circumstance short of war.
How small of a minority should be granted the power to deny the majority a say in their own national government?
The answer varies. For example, in the US, depending on what you are trying to accomplish it ranges somewhere among "half of the population", "that one guy at the FCC who writes the policy", and "1/3 of either house of Congress or 1/4 of the state legislatures", right?