That's interesting. If you do a 'man ls', the man page turns to black. But when you 'q', it goes back to red:). I think that "prompt" is basically good for the first command. Then you need to switch to something like 'system' as in this work-around:

#!/usr/bin/perl

use strict;
use warnings;
use ExtUtils::MakeMaker qw(prompt);

prompt("export PS1=\e[0;31m\][\\u@\\H\\W\]\$\\e]m");
system("ls");
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However, I like the idea of using 'ls' to return to the former color. It's quicker than restarting the terminal:).