The Linux equivalent of Inno Setup on Windows

Not sure if I understand right what is your problem. But, can it be solved adding an additional temporal separator? hence you can use the second separator to mark the separations, keeping the original separator untouched.

See this example where I add a "@" to each of the "|" so the input of the column command would be "xxx @| yyyy". Column will process the "@" keeping the "|" untouched:

~$ echo "foo | this is some text | bar" | sed 's/|/@|/g'  | column -s '@' -t
foo   | this is some text   | bar

I'm not sure why Perl isn't acceptable here. On the inputs you provided, this line gives the output you asked for:

perl -0777p -e 's/.* > (.*) joined the channel\.\n(((?!.* \1 (was kicked from channel\.|was banned from channel\.)\n).*\n)+?.*\1 disconnected)/\2/mg' irc.txt

The -e argument is exactly the first argument to your magicregextool except that I added the /mg regex modifier. This may not be "unmodified" but it doesn't seem unreasonable either. If you don't want to type in the whole line, how about this script as magicregextool:

#!/usr/bin/perl -0777p
BEGIN { $::arg = shift @ARGV; }
eval $arg;

Or even:

#!/bin/sh
perl -0777pe $*

Then you just type:

magicregextool 's/.* > (.*) joined the channel\.\n(((?!.* \1 (was kicked from channel\.|was banned from channel\.)\n).*\n)+?.*\1 disconnected)/\2/mg' irc.txt

Which is the same as your sample (again other than adding the /mg modifier).

An additional benefit to this is that if you are running multiple related search/replace operations on each file, you can put them together in the same script:

#!/usr/bin/perl -0777p
s/.* > (.*) joined the channel\.\n(((?!.* \1 (was kicked from channel\.|was banned from channel\.)\n).*\n)+?.*\1 disconnected)/\2/mg;
s/(some other\n)matched text/\1/mg;