"Shouldn't a torah based government actually be based on Torah?"
Yes, and Tradition reveals how that is - actually, plausibly - done.
"Which would put the kohens at the head of the judicial system"
A) Being able to identify a person as kohen would be the prerequisite for that. Let's deal with reality and what's realistic. The kohens we have today may be allowed to call themselves that, but couldn't actually prove their descent.
B) The kohanim were never at the head of the judicial system, the king (from the tribe of Judah) was. Moses told us to establish courts, but does not say only Kohanim may judge: indeed, most of the "Judges" (Shoftim) were not from Levi (there was one Judge from each tribe, f.ex Samson was from Dan.)
In addition to the Shoftim we obviously have "regular judges" which would be from any tribe, as far as we know.
Here is the hierarchy, as laid out in Jewish tradition:
1. king
2. high priest
3. prophet
And they all had different areas of authority in any case. Indeed, a father has more authority than the high priest does, when it comes the father's own child, hence "authority" can be relative.
The high priest
being Chief Justice, does not exclude men from other tribes from being judges, why you assumed that I did is curious? Moses does call for lower courts to officiate, which include heads of all the tribes.
Technically, speaking of l
aw given by God through Moses, a king is not spoken of for a chief justice. Moses did allow for a king, and gave instructions concerning that, but Moses did not set up a king for a governing official. A king was given upon request, but was not given until later, after Moses.
1Sa 8:5 And said unto him, Behold, thou art old, and thy sons walk not in thy ways: now
make us a king to judge us like all the nations.
1Sa 8:6 But
the thing displeased Samuel, when they said, Give us a king to judge us. And Samuel prayed unto the LORD.
1Sa 8:18 And
ye shall cry out in that day because of your king which ye shall have chosen you; and the LORD will not hear you in that day.
1Sa 8:19 Nevertheless
the people refused to obey the voice of Samuel; and they said, Nay; but
we will have a king over us;
1Sa 8:20 That we also may be like all the nations; and that
our king may judge us, and go out before us, and fight our battles.
1Sa 10:19 And
ye have this day rejected your God, who himself saved you out of all your adversities and your tribulations; and ye have said unto him, Nay, but set a king over us. Now therefore present yourselves before the LORD by your tribes, and by your thousands.
1Sa 12:1 And Samuel said unto all Israel, Behold,
I have hearkened unto your voice in all that ye said unto me, and have made a king over you.
1Sa 12:19 And all the people said unto Samuel, Pray for thy servants unto the LORD thy God, that we die not: for
we have added unto all our sins this evil, to ask us a king.
I do not see much that is good spoken through Moses concerning a future king?
Moses set the high priest as Chief Justice.
De 17:18 If there arise a matter too hard for thee in judgment, between blood and blood, between plea and plea, and between stroke and stroke, being matters of controversy within thy gates: then shalt thou arise, and
get thee up into the place which the LORD thy God shall choose;
9 And
thou shalt come unto the priests the Levites, and unto the judge that shall be in those days, and
enquire; and
they shall shew thee the sentence of judgment:
10 And thou shalt
do according to the sentence, which they of that place which the LORD shall choose shall shew thee; and thou shalt observe to do according to all that they inform thee:
11
According to the sentence of the law which they shall teach thee, and according to the judgment which they shall tell thee, thou shalt do: thou shalt not decline from the sentence which they shall shew thee, to the right hand, nor to the left.
12 And the man that will do presumptuously, and will not
hearken unto the priest that standeth to minister there before the LORD thy God,
or unto the judge, even that man shall die: and thou shalt put away the evil from Israel.7:
De 21:5 And
the priests the sons of Levi shall come near; for them the LORD thy God hath chosen to minister unto him, and to bless in the name of the LORD; and by their word shall
every controversy and every stroke be tried
The Levites were present it seems even in the lower courts. Josephus confirms this.