For starters, there is a reason why scripts are only permitted to run in the cgi-bin... it's what the cgi-bin is meant to be used for. If scripts were just allowed to run anywhere, then you'd find out that plain html files, text files, images, and everything non-script would fail to load because Apache would try to execute them as scripts.

As for using ScriptAlias for every single directory you want to run scripts in, why? That's what the Options directive is meant for! If your host permits it, stick an htaccess file in the subdirectory you want to execute scripts in, and place the following line(s) in it:

# .htaccess file

# You might need the following line. Maybe, maybe not
AddHandler cgi-script .pl

# Turn on CGI script handling in this directory
# and all subdirectories
Options +ExecCGI
[download]

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eval reverse@{[lreP
=>q{ tsuJ\{qq},' rehtonA'
,q{\}rekcaH },' tnirp']}[1+1+
1,1-1,1+1,1*1,(1+1)*(1+1)];
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