I think it’s only in the movies where Sam describes Athelas as a weed. In the books, Aragorn finds it on his own, and had to search hard for it in the dark, finding it only by its scent. It’s not a common plant, let alone invasive.
In Return of the King, we get:
Thereupon the herb-master entered. ‘Your lordship asked for kingsfoil, as the rustics name it,’ he said; or athelas in the noble tongue, or to those who know somewhat of the Valinorean…’
‘I do so,’ said Aragorn, 'and I care not whether you say now asëa aranion or kingsfoil, so long as you have some.’
'Your pardon lord!’ said the man. 'I see you are a lore-master, not merely a captain of war. But alas! sir, we do not keep this thing in the Houses of Healing, where only the gravely hurt or sick are tended. For it has no virtue that we know of, save perhaps to sweeten a fouled air, or to drive away some passing heaviness. Unless, of course, you give heed to rhymes of old days which women such as our good Ioreth still repeat without understanding.
When the black breath blows
and death’s shadow grows
and all lights pass,
come athelas! come athelas!
Life to the dying
In the king’s hand lying!
It is but a doggerel, I fear, garbled in the memory of old wives. Its meaning I leave to your judgement, if indeed it has any. But old folk still use an infusion of the herb for headaches.’
'Then in the name of the king, go and find some old man of less lore and more wisdom who keeps some in his house!’ cried Gandalf.
From this we can see that Athelas was still used as a folk-remedy in Gondor, to treat headaches, and to freshen the air: it’s not only useful against the Black Breath. We also see that the herb-master has probably not actually talked to Ioreth about Kingsfoil, because what she said when she was asked about it was not to draw any link between the herb and kingship: it’s Aragorn that does that:
'I do not know, I am sure, lord,’ she answered, 'at least not by that name. I will go and ask of the herb-master; he knows all the old names.’
'It is also called kingsfoil,’ said Aragorn; 'and maybe you know it by that name, for so the country-folk call it….
“Oh that!’ said Ioreth. 'Well, if your lordship had named it at first I could have told you. No, we have none of it, I am sure. Why, I have never heard that it had any great virtue; and indeed I have often said to my sisters when we came upon it growing in the woods: “kingsfoil” I said, “'tis a strange name, and I wonder why 'tis called so; for if I were a king, I would have plants more bright in my garden”. Still it smells sweet when bruised, does it not? If sweet is the right word: wholesome, maybe, is nearer.’
Even if Athelas was only introduced after the fall of Numenor, rather than before, it would have been part of the Middle-earth ecosystem for over 3,000 years, so in most countries would be counted as very much naturalised. That’s (probably) way longer than, say, wild cherries have been in Britain.
For that matter, we only have Aragorn’s word for it that Athelas came from Numenor at all. If Elrond isn’t reliable on these matters (and why on earth would Elrond not know about the ecosystem outside Rivendell? He was about 1800 years old when he founded the place), then how would Ioreth know?
I’m about Ioreth’s age, and I have no bloody idea if Danewort was really introduced by the Danes, or if the Watling Street Thistle was a Roman introduction, and both of those are way more recent!