Reply to myself…
After many months since my original post, I finally had the opportunity to look into this.
Logs produced by pure-ftpd in CLF (Common Logfile Format), lack the protocol version (as in “GET /somepath HTTP/1.0”).
I have tampered my logs to add the fake protocol “FTP/1.0”. A simple (and fast) sed line makes the workaround:
sed -i -e "s,\" 200, FTP/1.0\" 200,g" /var/log/pureftpd.log.1
I know this might not be the most elegant, and either pure-ftpd should add this to the log lines, or log-importer consider valid a log where the protocol version is missing. But in any case, this solves my problem.