Hmm, but you see, if you had attacked the citadel in the second year, you would have got it in the same year. That means that at the end of the second year (well, more precisely the beginning of the third) you were no longer at war with them.
But using spies, after two years you were still at war with the Aragonese, and therefore got excommunicated. I think it kinda makes sense, because the spies unlocking the gates succeeded in _the following year_. Had you done that in the first year (with the spies), you would have been fine, I'll bet.