JJ is different than KK on the turn on a queen high board. When you get threebet on the turn on a queen high board with JJ the percentage of times you are ahead is very low and the percentage of time you are going to improve on the river is only 2 outs. with KK percentage of time you are still ahead is obviously somewhat higher and percentage of time you are going to improve to a higher kings up which beats every other pair is also higher. they are not the same hand. On the flop they are basically the same in terms of value on the turn they are not.
This really isn't as true as you're making it out to be. Of course you have more value vs. QhXh and Q9 when you have KK as you either have more outs or you're still ahead, but the equity difference between the two hands AGAINST HIS ENTIRE FLOP C/R RANGE, which is what we care about, is ~5%. This isn't a huge difference by any stretch of the imagination and even if you think your opponent will 3-bet wide, you're either ok raising both, or you shouldn't be raising either. The edge vs. his range, giving him a strong range on the flop (sets, flush draws, 2pr, straight draws) for JJ on the turn is about ~58% (depending on if you think he c/r's all FD's or not) and for KK is about 63%. In either case, you have to very narrowly work up his exact turn 3-bet frequency to have it be in favor of raising the turn with KK but not JJ. The hands themselves perform much more similarly than you think against even a wide flop range, and the only way to change this is to randomly put hands like Q8, KQ, QTo in his flop range which, on this board texture, I would argue is not going to be happening. If you think you're inducing bad 3-bets with a raise, then you should raise both; if you think you're only going to get 3-bet narrowly by most of his value range, then you should not be raising with either.
Here's a very favorable calc that gives you an idea of the relative differences between the two hands:
Hand Pot equity Wins Ties
KcKs 66.87% 4,031 0
96s,97,98,T9,J9,Q9,K9,A9,22,77,99,T8s,*h*h,Q7s 33.13% 1,997 0
JcJs 61.11% 3,684 0
96s,97,98,T9,J9,Q9,K9,A9,22,77,99,T8s,*h*h,Q7s 38.89% 2,344 0
You have to come up with some pretty skewed calculations about his turn 3-betting range and frequency in order to make KK a clear raise but JJ a clear call. Basically, there's a reason that this hand is standard -- the range I gave LOL above is actually a bit narrow for him as I'd assume he has lots of 7x hands in his range as well that he'll bet on the turn and at the very least call a raise with. When we're strictly weighing the merits of a turn raise, the two hands are in the same category.