Yes, that's how it works, and it's not really very complicated. Flash in Rattlechains, Wanderer triggers. Allow trigger to resolve, then sacrifice Wanderer. The stack isn't "Lock everything in and then it all resolves", you get to respond between things resolving.
CMC never changes. CMC is the sum of the symbols in the top right, no matter what you paid. Blasphemous Act has a CMC of 9 whether you paid 1R, RR, WUBRG, or two fishsticks to cast it.
The stack does not resolve, because it is a game zone. OBJECTS on the stack resolve, one at a time, and after any object on the stack resolves all players have priority to do stuff again before the next one does.
Pro-black means Karmic Guide cannot be Damaged, Enchanted/Equipped/Fortified, Blocked, or Targeted by any black spells, black permanents, or abilities from black sources. Altar's Reap does none of these, and so Protection does nothing.
No, it stops targeting AND enchanting. If I give pro-green to your guy with a Rancor on it, the Rancor can no longer legally enchant it so it falls off. It's why the white enchantments that give protection have to say 'this effect does not remove CARDNAME'.
You can, because of the way it's worded (an ETB and LTB trigger, rather than an ETB with a duration), but you'll want to be using either a delayed blink like Long Road Home, or a sacrifice/bounce. If you just use a normal there-and-back-in-the-same-spell blink like Essence Flux, you'll have to target a spell again when Queller enters, so unless there's ANOTHER legal target for that trigger, you'll just use ETB 2 on the spell you want to perma-exile, then LTB1 and ETB1 do nothing.
RTFC happens to everyone.