That can delete too many lines.

01 keep 
02 keep        <- gets discarded by your code.
03 keep        <- gets discarded by your code.
04 keep        <- gets discarded by your code.
05 keep        <- gets discarded by your code.
06 keep        <- gets discarded by your code.
07 discard B5
08 discard B4
09 discard B3
10 discard B2
11 discard B1
12 somepat
13 somepat
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That's in addition to the problems with $.-5 going negative.

By the way, splice would be more efficient than delete since it wouldn't shrink the allocated buffer.

I'm also trying to get the (-d) to be a stand-alone flag. What would be the best approach to this?

    'd!'      => \$delete,
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-c ./someconfile

That's weird. Why not just print to STDOUT and redirect output? It's way more flexible at no cost.

perl dellines.pl -i somepat -d > someconfile
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The name of the option doesn't even make sense. It's an output file, not a config file as far as the tool is concerned.