Firstly I'll state that I'm no expert on medieval law so take my input with a grain of salt.
IMO, the situation is somewhat ridiculous. Firstly, a citizen (I'm assuming a peasant) would have to be in a very unique position to be able to take the noble into custody in the first place. It would require that the noble not be armed and not have any guards and be cowardly enough not to fight the citizen. This is all very unlikely.
But let's say that somehow he's managed to capture and subdue the noble. The next challenge would be getting the noble 'to justice'. Any effort to do so is incredibly risky on the citizen's part. The noble could basically call on any person of any training or knowledge, to cut the citizen down. And few would balk at the citizen's claims of 'justice', especially when the noble can just offer a reward for cutting the citizen's head off.
But again, let's assume he's negotiated these two HUGE obstacles and brought the noble 'to justice'. The justice then says, "By what right do you lay hands upon a noble of the realm?" And the citizen promptly gets his head cut off. Justice be damned. The nobility maintained control primarily through corruption, ie. it mattered more who your friends were than who were your enemies. And few arbiters of justice are going to take the word of anyone of lower status, let alone some rag-tag peasant, against the noble. Hell, the arbiter of justice probably wouldn't even hear the citizen out before stepping in and cutting his throat for daring to lay a hand on his new best friend, the noble.
But, again, let's say he took the noble to some uppity, self-righteous, lawful stupid paladin, and the paladin heard the citizen out and demanded a lawful investigation which, if the facts were determined to warrant it, would lead to a trial.
The paladin is a dead man. Period. Right or wrong, god or no god, the realm will go to war to get the noble back and punish the paladin for treason against the realm and cut off his head and put it on a pike. The citizen's body would just never be found as he wouldn't even get that honour. Hell, even if half the realm HATES the noble's guts and WANTS him dead, they'll go to war to get him back solely on the basis that some upstart citizen and pompous little paladin thought they could defy the status quo. The people in power would punish both of them, and wholesale slaughter just as an example, any who stood with them. And quite frankly, nobody would stand with them for just that reason.
But... I'm guessing that your real question is that if all of the above was irrelevant, and the situation had actually gotten to the stage of a trial, in a world where nobility could be put on the stand like this at all (which again is so unlikely it's not funny), then I would consider two things:
1) In a setting that uses more modern sensibilities of right and wrong, as it seems this situation demands, then I'd probably go so far as to say that the law would require the nobility to submit to magical testing, after all, if all the layers of protection against this sort of thing happening have already been stripped away, then logically there isn't going to be a hail-mary for someone at the last minute.
2) If you want to have it that the nobility have a level of power similar to what they had in history, despite having gone this far, then I would say that no matter what, the nobility would've had it written in law that they have this hail mary for just such a situation, and nothing short of damning evidence (in which case you don't need the testimony) can trump it.