On a large number of bans do not the above posted scripts run the risk of the issuer exceeding their SendQ limit server-side for most networks - hence them getting booted off?

I don't know where mIRC's internal anti-flood system works with regards to this, but my suggestion would be the following:

Where possible consider using services' commands to perform this action (on networks with service bots similar to QuakeNet's "Q" or DALnet's "ChanServ" there is usually a method to clear a channels modes with a single request to a service bot (re-setting a few channel modes is a fairly trivial affair if it clears all modes).

Otherwise, perhaps throttle the mode changes with a timer, or dump the commands to a file and play it with a reasonable delay setting.