Yes, they could be subject to prosecution if they certified him (ex. Pelosi) as being Constitutionally qualified knowing that he was not...and certified the E.C. votes knowing that they should not have been (i.e. Congress). The difficulty would be in proving that they did so knowingly and with intent to circumvent the Constitutional requirements.
I am wondering if this judge's terminology, to wit: might cause embarrassment to Congress .... implies that he actually sees merit, that he agrees that BHO is either Indonesian OR Canadian OR Kenyan OR 'whatever' -- but NOT American....