You can already do it, but it's called something else.
Instead of updating a certain hunk (which is fundamentally wrong, since it depends on "diff" even working on that file), you can tell git-update-index to update a certain _state_ for an arbitrary number of files. Namely:
git-update-index [--cacheinfo <mode> <object> <file>]*
However, that obviously is very much a _plumbing_ command, and you need to have some higher-level GUI on top of it to actually pick out the chunks (if that is what you want) and generate the object(s) associated with the file(s) with only those chunks and then do the above "install this state into the index/staging area/whatever".
In other words, git already supports this on a _technical_ level, but does not have the high-level interfaces for it, and quite frankly "git-update-index" _shouldn't_ have the high-level interfaces for it. It's designed to be the low-level technology, not the actual interface.
I think it's more appropriate for a GUI front-end, frankly, but you could script it fairly easily with whatever your favourite patch editing tool:
(a) Generate the "result" file you want in /tmp or something, using patch
editing tools to extract a partial patch and apply it to the original
file. (b) Use "git-hash-object" to create the backing store object, and get the
SHA1 for that file. (c) Use "git-update-index --cacheinfo <mode> <sha1> <filename>" to
populate that new entry of yours into the index. (d) Do (a)-(c) as many times as you like to handle all the files you
want to commit, and then just call "git commit"iow, it's not hard, but no, git on its own is _not_ a patch-based system, and doesn't do things hunk-for-hunk. You need that "hunk selector" interface on top of it.