Lucene uses an append only strategy, which means that when a new version of an old document is added, the old document is marked as deleted, and a new one is inserted into the index. This way allows Lucene to avoid rewriting the whole index file as documents are added, at the cost of old documents physically still being present in the index - until a merge or an optimize happens.
When you issue expungeDeletes, you're telling Solr to perform a merge if the number of deleted documents exceed a certain threshold, in effect, meaning that you're forcing an optimize behind the scenes as Solr deems necessary.
How you can work around this depends on more specific information about your use case - in the general case just leaving it to the standard settings for merge factors etc. should be good enough. If you're not seeing any merges, you might have disabled automatic merges from taking place (depending on your index size and seeing hundred of thousands of deleted documents seems extensive for an indexing processing taking 2m30s). In that case make sure to enable it properly and tweak it values again. There's also changes that were introduced with 7.5 to the TieredMergePolicy that allows even more detailed control (and possibly better defaults) for the merge process.
If you're re-indexing your complete dataset each time, indexing to a separate collection/core and then switching an alias over or renaming the core when finished before removing the old dataset is also an option.