Code:
on *:START: .unset %nickflood.*
on *:NICK: {
  [color:blue]var %chan = #channel1,#channel2[/color]
   if ( (($newnick ison $gettok(%chan,1,44)) && ($me isop $v2) && ($newnick !isop $v2)) || (($newnick ison $gettok(%chan,2,44)) && ($me isop $v2) && ($newnick !isop $v2)) ) {
    inc -u10 $+(%,nickflood.,$address)
    if ($($+(%,nickflood.,$address),2) = 3) {
      if (($newnick ison $gettok(%chan,1,44)) && ($me isop $v2) && ($newnick !isop $v2)) { msg $v2 $newnick Excessive Nick Change will NOT be Tolerated! This is your First & Last Warning. }
      if (($newnick ison $gettok(%chan,2,44)) && ($me isop $v2) && ($newnick !isop $v2)) { msg $v2 $newnick Excessive Nick Change will NOT be Tolerated! This is your First & Last Warning. }
    }
    elseif ($($+(%,nickflood.,$address),2) > 3) {
      if (($newnick ison $gettok(%chan,1,44)) && ($me isop $v2) && ($newnick !isop $v2)) { kick $v2 $newnick Excessive Nick Change! }
      if (($newnick ison $gettok(%chan,2,44)) && ($me isop $v2) && ($newnick !isop $v2)) { kick $v2 $newnick Excessive Nick Change! }
    }
  }
}

^ that well ignore them if there an op but well kick em from the other channel if they are not an op


Code:
on *:START: .unset %nickflood.*
on *:NICK: {
  [color:blue]var %chan = #channel1,#channel2[/color]
   if ( (($newnick !isop $gettok(%chan,1,44)) && ($newnick !isop $gettok(%chan,2,44))) && ( (($newnick ison $gettok(%chan,1,44)) && ($me isop $v2)) || (($newnick ison $gettok(%chan,2,44)) && ($me isop $v2)) ) ) {
    inc -u10 $+(%,nickflood.,$address)
    if ($($+(%,nickflood.,$address),2) = 3) {
      if (($newnick ison $gettok(%chan,1,44)) && ($me isop $v2)) { msg $v2 $newnick Excessive Nick Change will NOT be Tolerated! This is your First & Last Warning. }
      if (($newnick ison $gettok(%chan,2,44)) && ($me isop $v2)) { msg $v2 $newnick Excessive Nick Change will NOT be Tolerated! This is your First & Last Warning. }
    }
    elseif ($($+(%,nickflood.,$address),2) > 3) {
      if (($newnick ison $gettok(%chan,1,44)) && ($me isop $v2)) { kick $v2 $newnick Excessive Nick Change! }
      if (($newnick ison $gettok(%chan,2,44)) && ($me isop $v2)) { kick $v2 $newnick Excessive Nick Change! }
    }
  }
}

^ that well ignore them if there an op on ether channel

* again untested