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Today, we had a tournament where i finally got to play with 6th ed rules Ive read so much about, however, being that i play orks, i felt kinda nerfed because my melee became a secondary function of my boyz... however, after shooting the crap out of a space marine assault squad and them failing their leadership, they started running away. I assaulted them and thought to myself
"what actually happens when you assault a fleeing unit? "
The Judge told me that they roll to regroup and if they do, resume assault as normal, without overwatch since they are already in assault. If they don't and you make it into h2h, the assaulted unit is gone forever.
The entire enemy squad was destroyed (because 30 boyz with shootas iz still 30 boyz ) but if they had overwatch, i would imagine that it might have turned out a little differently, so. What do YOU think of this ruling, or what are your opinions on this subject matter. I personally think that if you're hitting someone while they are retreating, your attacks should be resolved first regardless of initiative (except initiave 1, becasue those move slow enough for them to turn around when they hear it),

No opinions needed; the rules are completely clear and explicit. See pages 30, 31, and 33.

Page 30 states clearly that fleeing units can shoot (and are allowed to Overwatch), but can only Snap Fire.
Page 31 states that when you assault a fleeing unit, they get a chance to Rally, on normal LD (even if under 25% starting strength, when they'd normally only be able to Rally on Insane Courage double 1s). If they fail, they die. Page 31 also tells you exactly when.
Page 33 tells you that units which have And They Shall Know No Fear automatically pass tests to Rally.

Thanks! I'll note it for the future

Mannahnin is correct, I have only one thing to add that the judge missed; The SM group that was falling back still would be able to shoot overwatch as you declare you charge.

The judge apparently had most of the rules wrong, based on what the OP wrote.