As for Metataks, I suspect that BioBob didn't plan any of the things you've been discussing in the last few pages, like saving Mr. Fat, preserving Friend-ologist, and freeing (?) Rusty.
The question is about Sir Lock – killing him is not mandatory for completing the map, and neither are the two locations with their associated quest markers. If you don't have access to them, it doesn't affect the completion of the map in any way; no bonuses are lost. This is strange, because every other part of the map either directly participates in the completion or provides some kind of bonus.
Unlike the situation with Rusty and Dess, where Nautilus simply didn't see (or hid?) such possibilities (which is not surprising, as only Nasos noticed this 5 years after the map was created), in the case of Sir Lock, Nautilus consciously sacrificed the locations associated with him and the integrity of the map.