You're better off writing a script to look-up organism or species information from the GI numbers than changing the input to makeblastdb. makeblastdb needs sequence identifiers to be unique and your changes will result in makeblastdb erroring out. You can work around that by adding suffixes to org/species names, but that's too much effort invested in a result that won't hold up in cross-database look-ups.

A simple query to NCBI to getch the GenBank or GenPept record should give you access to any attribute you need.

Another way is to download the BLAST taxonomy database as described here. Then use the "sscinames" output format option for BLASTP to get the species name in the BLAST result. The species name will be an additional column. If you want the species name information in the identifier, you can parse the BLAST output and concatenate the sequence identifier and the species name.