I think part of the problem is the fact that there's a real phenomenon that's important to talk about and describe, but rather than invent a new term, that the word 'racism' has repurposed to describe it instead.
200 years ago, everyone would have understood "racism" to mean what you have implied it means: conscious individual racial prejudice. And of course, one problem that (say) blacks in the US face is widespread, individual, conscious racial prejudice.
But there's yet another problem blacks face: the mechanisms of society as a whole disproportionately cause problems for black people, even when nobody involved is consciously prejudiced. When this was pointed out, people would respond, "But nobody in this organization is prejudiced". Well, it doesn't matter if the people are prejudiced or not, the emergent property of the system as a whole affects black people as though it was set up by people who are racist; and so the system is called "racist", even if nobody in it is trying to be racist.
I think the argument here is the same: Iranians are facing persecution for no other reason than the country they were born in. It doesn't matter if people making the policies of the US government is prejudiced against Iranians as individuals or not; the net effect is the same.
(FWIW I think the concept of "institutional racism" is useful, but the overloading of the term 'racist' to describe it is counterproductive in the long run.)