Yes, that text file can be deleted. I think it is just there to keep people from deleting the dynamic folders, but the files themselves can all be deleted.
Do you have a save before entering the spider forest? If you reload, does this problem still occur?
Have you visited any of the other areas around the village? Doing things in a different order may help, or at least put off visiting the problem area for awhile.
The spider queen should approach in a cut scene when you get close enough. This is not being triggered properly, so she does not turn hostile.
