Executing ./ Commands Through Hackers Shells

I've been concerned about executing commands through (./) using php and perl shells on the server

a new way of hacking these days is using perl shells , even if the perl was terminated on the server ,, or was forbidden for users
hackers upload a (perl) program to the server to use it instead of the server's own perl

any way ,,

chmoding the (ls-cat-more-less) to 4750 seems to give permission denied when exeuting these programs on the server
but the hackers also found that they could upload their own ls-cat-more-less programs and use them instead of the server's

they also could rename them ls==>ki or anything and use them like this

./ki /etc/valiases -alXrt
and the commands work like charm for them

./ <<--- this command uses the sh program on the server ,, ((sh which refers to bash on most servers))
so

./ki
is the same as

sh ki

and

bash ki

so i tried chmoding sh with 4750 and that killed the exploit

i was concerned about cpanel's and the website's functionality
so i tried changing an accounts password and creating a database ,, they both worked fine

so ,, if u thing chmoding 4750 sh is a bad idea please let me know

and if you know any other ways of disabling all the perl scripts on the server