Usually I feel I have something to add, but you said it all pretty much here!
I think it's important to remember that while Reptile is almost indisputably 12th on the tier, Baraka is arguably as high as 6.
I'd put him around 8th, making him low mid-tier. Therefore, he SHOULD win this match.
REPTILE
Invisibility is your key to victory. And Baraka doesn't have too many weapons to keep that from happening. When you're invisible, you really can control this match. Anti-air roundhousing Baraka is pretty easy on OG, but a nightmare on MKAK (maybe just me?). As soon as you go invisible, expect Baraka to throw a blade spark in an attempt to find you. Slide him when he does. Also, crossovers when you're invisible really confuse Baraka. Forceball and spit are pretty good vs him because his spark is slow, but only do them from far away (and preferably while invisible!).
BARAKA
As long as you're always chasing Reptile down, you should be fine. All blocked slides can be punished with shredder for big damage. The goal is to pressure Reptile with your CQC. Baraka's fast walk, and awesome sweep will make getting in possible. Baraka can easily anti-air roundhouse all the ninjas as well. Blade spark is good if Reptile wants to trade projectiles from afar. Do it too much though and Reptile will slide you. Only use the shredder when you know it will score, because Reptile's forceball/uppercut combo does massive damage (for Reptile at least!)
Ahh back in the day I thought these were the 2 worst fighters in MK2, and that this was a very even match.
Welcome to reality- Baraka wins 7-3.