After some investigation, unfortunately logstash-input-sqlite uses the same JDBC driver (an older version though, but still includes the cleanup) under the hood. Meaning that even if the "Missing Valuefier handling for full class name=org.jruby.RubyObject, simple name=RubyObject" bug was fixed you would still get the .so file delete issue.
BTW, the "Missing Valuefier" bug is because the input has not been updated to convert some JDBC datatypes to datatypes that are acceptable to the newish Java Event (each acceptable datatype has a corresponding Valuefier).
If you are considering exporting to CSV then you should also consider exporting to one or more Apache Derby DB files.
That said, we have not verified that multiple JDBC inputs work satisfactorily on all supported DB technologies. We simply do not have enough time to do this - we rely on the help of others (e.g. you) and offer this kind of help in return.