Can I remove binary log files not listed in mysql-bin.index?
You can also try purge binary logs before '2016-04-29 08:00:00'. I sometimes find one works when the other doesn't for some reason.

Failing that just delete them with rm like you said. It's not technically correct, but it shouldn't be a problem (I did this frequently in the past before I learned about the PURGE commands, and never had any problems).

Of course you also want to make sure you have expire_logs_days set as well to keep them down in future.

I also just saw this note:


  Prior to MySQL 5.1.24, PURGE BINARY LOGS TO and PURGE BINARY LOGS
  BEFORE did not behave in the same way (and neither one behaved
  correctly) when binary log files listed in the .index file had been
  removed


for some reason I don't have access to the 5.0 page to check what that says.