If I understand your question correctly, then you want to hide the use of these commands from being displayed on the channels.
In this case, you need to install the "halt" command at the end of the script. More on this here: https://en.wikichip.org/wiki/mirc/commands/halt or https://www.mirc.com/help/html/index.html?halting_text.html

Code
on *:INPUT:*:{
  if ($1 == !ifo) { .echo -a 00,04 cac222a  | .whois $2 }
  if ($1 == !sj) { .sajoin $2 $3 }
  if ($1 == !sp) { .sapart $2 $3 }
  halt
}

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