The SSTableLoader won't have any bad effect by terminating it. You can run it over the same set of SSTables multiple times without having to worry about data corruption.
The follow on SSTable index build happens automatically in the background. You can increase the number of concurrent compaction threads. Multiple indexes can be built simultaneously.
Building indexes is time consuming and often takes longer than ingest, but the data will be available to read and write.
You could manually stop the index_build, I'm not sure that that will cause the SSTableLoader to exit (because I've never tried it) but you'll then need to tell cassandra to rebuild the index using nodetool.