The problem isn't in the elapsed filter. You can use Logstash with dotted fields with no problems. You just can't send an event to Elasticsearch where any field names contain dots.
You'll need to reformat your data, whether with mutate filters (adding and removing fields as necessary), or at the source.
We've bandied about a "de-dot" filter or codec to cover instances such as these. Perhaps it's more pressing than we thought.