What you might want to try is to mount the game folder using ciopfs (a case insensitive filesystem for linux) - I've done this then installed both Rogue Rebalancing and Sword Coast Stratagems and they run without a hitch. As a plus you don't even need to use tolower! I'll provide some instructions for you guys, assuming the use of Ubuntu and the enhanced edition because that's what I have. # are my instructions and the lines below are the commands to run.
# ==========
# First open a terminal and then install ciopfs:
sudo apt-get install ciopfs
# Then move to the level above the install directory and create a hidden foilder for ciopfs to use:
cd ~/.local/share/steam/steamapps/common
mkdir .BGEE
# Copy the game folder to another hidden folder and then clear it (so ciopfs can mount to it):
cp Baldur's\ Gate\ Enhanced\ Edition .oldBGEE
rm -r Baldur's\ Gate\ Enhanced\ Edition/*
# now mount the hidden folder with ciopfs and copy back the original data
ciopfs .BGEE Baldur's\ Gate\ Enhanced\ Edition
cp .oldBGEE/* Baldur's\ Gate\ Enhanced\ Edition
#==========
Now you should be able to test the game works, then extract your mod files to the "Baldur's\ Gate\ Enhanced\ Edition" folder as normal and install all the mods you want without the need to use tolower before weinstall.
#==========
# IMPORTANT
#==========
Once you have tested the game runs then there is one more step to make the ciopfs baldurs gate permanent; edit your /etc/fstab file (try the command "sudo gedit /etc/fstab" without quotes) and copy in the following to mount the ciopfs folder to the game directory on login (assuming you have the default steam install). Make sure to modify "USERNAME" to be your USERNAME.
/home/USERNAME/.local/share/steam/steamapps/common/.BGEE /home/USERNAME/.local/share/steam/common/Baldur's\040Gate\040Enhanced\040Edition\ ciopfs allow_other,default_permissions,use_ino,attr_timeout=0 0 0
And thats it - enjoy!
Note: I only know about this because of a similar issue faced by the CIV5 modding community after the linux version came out. See the steam community discussion
http://steamcommunity.com/app/8930/discussions/0/540744299996631016/ for the original source of these instructions.