If the C binary is giving you trouble, and all it's doing is pulling stuff out of a database, then you might consider factoring the binary out, and replacing it with DBI (unless there are problems with getting DBI and the appropriate DBD modules installed, in which case, you might want to see what's needed to solve those problems...)

Apart from that, you don't show any code, so we don't know why the perl script aborts. Maybe it's because the script is written like this:

my $failure = system( "c_binary ..." ); # system returns exit status
die $! if ( $failure );  # which is normally non-zero on failure
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If that's the case, all you need to do is replace "die" with "warn", and redirect the STDERR from your script into a log file -- e.g. if you are using a bash or similar type of shell:

  your_perl_script ... 2>> log.file
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