The passage you are listing does not actually imply that Judas was doomed to destruction so that the scriptures might be fulfilled.
In the ESV for example
While I was with them, I kept them in your name, which you have given
me. I have guarded them, and not one of them has been lost except the
son of destruction, that the Scripture might be fulfilled.
Note the use of commas:
I have guarded them, ... , that the Scripture might be fulfilled.
Here the verse is stating that Jesus kept and guarded the disciples in order to fulfill the scriptures. The fact that Judas was lost is mentioned as an aside/footnote and not as a necessary condition for the fulfillment of scriptures. So at least here, no claims are being made that Judas was predestined for destruction as part of a grand design.
I think to find the answer to the heart of your question, however, you should read Romans 9-11 (exerpt below)
10 And not only so, but also when Rebekah had conceived children by
one man, our forefather Isaac, 11 though they were not yet born and
had done nothing either good or bad—in order that God's purpose of
election might continue, not because of works but because of him who
calls— 12 she was told, “The older will serve the younger.” 13 As it
is written, “Jacob I loved, but Esau I hated.”
14 What shall we say then? Is there injustice on God's part? By no
means! 15 For he says to Moses, “I will have mercy on whom I have
mercy, and I will have compassion on whom I have compassion.” 16 So
then it depends not on human will or exertion,[b] but on God, who has
mercy. 17 For the Scripture says to Pharaoh, “For this very purpose I
have raised you up, that I might show my power in you, and that my
name might be proclaimed in all the earth.” 18 So then he has mercy on
whomever he wills, and he hardens whomever he wills.
19 You will say to me then, “Why does he still find fault? For who can
resist his will?” 20 But who are you, O man, to answer back to God?
Will what is molded say to its molder, “Why have you made me like
this?” 21 Has the potter no right over the clay, to make out of the
same lump one vessel for honorable use and another for dishonorable
use? 22 What if God, desiring to show his wrath and to make known his
power, has endured with much patience vessels of wrath prepared for
destruction, 23 in order to make known the riches of his glory for
vessels of mercy, which he has prepared beforehand for glory— 24 even
us whom he has called, not from the Jews only but also from the
Upon request I will add a bit of my own interpretation here, although I would encourage the reader to form their own opinion by reading carefully, thinking deeply, and taking the whole council of scripture into account.
Additionally, a lot of arguments about Arminianism vs Calvinism and predestination/election boil down to these passages, and it is not my intent to engage in that sort of debate (volumes have already been written over this debate).
From my perspective, Romans 9-11 (as well as other passages such as the one mentioned in Tony's answer) seem to clearly point to the fact that God creates both
vessels of wrath prepared for destruction and
vessels of mercy, which he has prepared beforehand for glory. So why, as your question implies, would God make someone 'doomed for destruction'? This gets at the question's implicit framing of "free will" vs "determinism", but I personally think this is a false dichotomy, the answer, in my opinion, is both.
Very briefly/imprecisely: God created us and gave us free will. The Bible, however, is very clear that, out of our own free will, we all will choose sin over God, condemning us to hell. Christ died to pay the penalty for our sins and redeem us from this state, but, due to our sin natures, we all naturally choose to reject this atonement. God, however, out of his own grace, intervenes for some, allowing them to see the error of their ways and to repent.
The ones that choose sin willingly are the
vessels of wrath and, of their own free will, are unrepentant. (the free will part) You could say God
prepared [them] for destruction in the sense that he a) created them and b) knew before they were created that they would (freely) choose to be unrepentant. (the pre-determined part)
Now for the
vessels of mercy we have the people that God a) allowed to see their true sinful condition (the pre-determined part) and that then freely chose salvation (the free will part).
So, in short, my answer would be yes. God, in a certain sense, creates vessels of wrath like Judas, and they do fulfil a purpose in his plan. This is not cruel or incompatible with free will, however, as these people freely choose sin and freely choose to stay in sin. From our side of the cosmic coin this looks like free will, but from God's side of the coin (outside of time and with perfect knowledge) this is all foreknown and thus looks like predetermination/predestination.