Indeed, maybe backticks (``) could be used on this line directly:
$isacon = `/apps/home/pfuser/scripts_56/GENERAL/pers_lookup.csh $sids[$index]`;
Backticks, like the double quotes (""), interpolate the string, which means that they translate every variable to its value. Then they run the string as a shell command and return the output.
Since you are not sure about the programmer's intention, you should still test it first with double quotes and check the result, for example by printing it, and only then you should run it with backticks or system.
Read more about all the different types of quotes here: Quote-like Operators in perlop.