How so?
I think, but do not know, that this refers to the Faith’s centuries-old habit of blessing Targaryen incest but withholding their blessing from Lannister incest.
The High Sparrow cannot personally be a hypocrite in this regard, as he was not there, but the Faith as a whole absolutely is.
There were extenuating circumstances in the form of giant fire-breathing murdersauruses, of course.
And I think the High Sparrow would absolutely admit that the Faith has been hypocritical in that regard – his whole agenda is based on an argument that the Faith has been corrupted by secular politics and needs to reassert its independence to as to pursue an agenda of moral reform.