After the war they may be seen as British rather than Americans
How can not granting them citizenship in the first place possibly be enforced? How do you define someone as Loyalist? 500,000 may have supported the British but (at a guess) no more than perhaps 10-20,000 actively fought for them, so how do you dictate who counts as a Loyalist after the war? Get neighbours to vouch for them? In that case you're going to end up with an 18th century McCarthyism, where people will snitch on anyone they don't like just to get them in trouble with the authorities. Just punish those who fought? Then you're not talking about Loyalists any more, just soldiers. And for all of this, why should political affiliation deny you citizenship? Isn't that a violation of the principles of the Declaration of Independence anyway? And there's a real risk that the more pro-British areas, on being told that they are going to be actively outcasted by the state and have all of their rights denied, would declare independence from the newly independent state, dropping the USA into a whole new civil war.
There's no realistic way that you can possibly deny citizenship after an independence war to everyone who supported the losers. There's just too many problems with making the system work. The reason why the United Empire Loyalists fled to Canada OTL was a mixture of political affiliation and fear for their safety, not because the new US government literally transported them to the border and told them never to return. If you want to make the Loyalists stay in the USA, you need to find a way of overcoming those two issues, not the government's stance.
Perhaps, let us say, instead of the OTL vengeful attitude toward the loyalists, Congress instead adopts a reconciliatory approach and passes an Act of Oblivion. ?
The US Government may have been harsh to those it believed Loyalists, but it was more than that which made the Loyalists flee, as above. You need to stop common citizens from attacking Loyalists in the street, and you need to make the Loyalists want to stay as opposed to seeking a new life under the flag they love.