is there a skyrim script compiler that can batch an entire folder of files?

The reference compiler already supports batch compilation. All that you need to do is replace the script name argument with the path to the folder and add another "all" (without the quotation marks) as an argument. Basically invoke the compiler with:

PapyrusCompiler.exe  -f=TESV_Papyrus_Flags.flg -i= -o=
 -all