There is no good solution in Craft 2.x, but you probably can put together a plugin or a console app that does what you want it to do. Here's all the background info you, hopefully, need.
AssetIndexTool class and are operating on that via
Craft Asset indexer operates strictly on the data in
craft_assetindexdata table. When you start an indexing task, the very first thing it does is query the Asset Sources for all the actual files that are there, stores a list of them in the said table and from that point on uses that table to reference what files have been indexed and which not. As it does it, Craft also creates all the folders already (because, apparently, a long time ago it seemed like a good idea to me).
After that, the tool returns an array for each of the steps it needs to take, where one step is generated per file and also an additional "overview" step at the end. Each array entry basically contains parameters that you should throw back at the Index Tool.
What you're interested in each of those "step" arrays (if you want to understand how the whole process works) is
sessionId variable there to track the indexing session in the indexing table, the
sourceId variable so you know which source you're operating on and the
offset variable that tells the Index Tool which file in the indexing table to look up and actually index.
You should definitely also follow through with the last overview step. Never mind that it presents the user with a HTML dialog for all the files that are in the DB but are not present in the source, but, more importantly, it cleans up the asset indexing table and removes the obsolete data in there.
The great news is that it will be significantly less convoluted and way more accessible programmatically in Craft 3.