Ah, sorry, I misunderstood what you meant you said it was a common poetic device; I thought you meant mispronouncing a word to get it to rhyme was a common poetic device as it sometimes is in humorous verse, like limericks, say. (OK, let's not get started on limericks ...)
I'm with you now (I hope). You're saying that you intend "the contrary" to be a group of people. And like that, I agree, the metre and rhyme are fine.
Confusion arises, I think, because the sentence makes sense on both usages: "she queries (challenges) new saints proof that might show the opposite" and "she queries new saints proof to the contrarians". The former meaning, used with phrase "to the contrary", being a very common construction.
I wonder if there's a rewording that excludes the reading you don't want?
I also wonder if "the contrary" means quite the same as "the contrarians". Even had I known that there was a committee whose job it is to disprove miracles, I'm not sure I'd know they were being referred to by "the contrary" (pronounced as you intend), as 'contrary' has (to me anyway) a somewhat derogatory undertone, a sense of those who are awkward and don't behave as expected / desired / asked.
Anyway, I don't know the full details of the canonisation process. I was brought up Catholic and went to Catholic schools, but they didn't teach us this. Searching the web for a bit I can't find a description of a committee whose job it is specifically to oppose claims to miracles, so I don't know if they're normally referred to as the 'contrarians' (which might make the link easier to make for those who know this). I do wonder what percentage of your readers will make the link you intend here. Obviously, not having made it myself, I may well be biased in my estimates