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I have a server that uses ScriptFTP for backup purposes. The directory tree is very deep and so the 260 character limit is a serious problem for me, because we use such a folder structure.

Is it possible to disable this path length protection?

I am running Windows server 2012 R2 Standard with about 5TB of data that is incrementally backed up every day to an offsite location.

The 260 character limit is a windows limitation. Applications (such as ScriptFTP) are limited to use 260 characters in a path:
I have an AD set up on windows and 260 characters path length limitation is removed. My AD works with no problem with paths exceeding 260 characters.

HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\FileSystem\LongPathsEnabled set to 1
Ok, thanks. I will add this to the list of issues to investigate a bit further for the next release. There may be a workaround to the API limitation.

is there an update supporting this feature coming out in a foreseeable future?
No, sorry. This seems to be a Windows limitation and we cannot fix this from ScriptFTP