if (!$timer(X)) { msg $nick wait a while } | else { msg $nick you can so it now }

NB: i followed exactly what you showed in your code which appears to tbe the opersite of what you said.
ie: your code says if the timer is not functioning then they must wait, to reverse the effect simple remove the ! from $timer() (the ! is a NOT)

nb: you should name the timer a specific name rather than relying on the automatic timer numbering
ie:
/timerFRED 1 10 echo -a Saying Fred
//if ($timer(fred)) { echo Timer Fred is running } | else { echo Timer Fred is not running }