I think people are maybe over-thinking this a bit. Let's break it down:
Question 1: what to do about the WSG? I don't think it matters. It's tricky to make travel depend on finishing the quest, since one method of finishing the quest is to prevent its existence. So I suggest either a) don't do anything, and let the implicit assumption be that Moira will get someone else to help her if the LW fails to; or b) make it a requirement, and make a consequence of the "dream-crusher" solution be that there are NO survival skill books, anywhere. After all it's a jerk move, and you get a nice perk for it. Reasonable trade-off, I say.
Question 2: does the bullet to the brain knock you back to level 1 for the NV half of the game? I think NV itself suggests yes, because the whole premise is that the courier is an experienced, skilled traveller, yet it starts you at level one. Plus, OWB lore establishes that the brain injury has some very unusual side-effects.
However, this very much comes down to player choice, and both choices are reasonable in a project like this. I think the mod should allow either choice to be selected at the beginning of the game.
Question 3: what to do about leveling and XP rates? Well, this depends entirely on the answer to question 2. If the player chooses the "full-amnesia" start-over option, nothing has to be adjusted; if the player chooses to keep their skills, there will be issues. But, as was mentioned above, those issues can be dealt with by the player making that choice, using any number of other mods that adjust leveling and skills. I use slow-leveling mods anyway, because I think the early/mid game is more balanced, and I think leveling up should be a rare, awesome event. Others may disagree, preferring to become a demi-god faster. To each his own.
In sum: I don't think the TTW devs need to cater to one or the other group. Let people make a choice as to Question 2, and players' imaginations and mods can handle the rest.