It's to trick 8 year old ratbots and zbots (and other proxy-based cheats) into reconnecting to themselves.
The operation of these proxy-based bots works something like this:
-You load up an external stand-alone program. The program can make sense of the network traffic between client and server, and can change the behavior of your client through the same information protocol.
-You instruct the bot(or external program) that you will be connecting to GT Pub1(just as an example, this isn't a walkthrough kiddies) at 69.93.11.66:27911
-Once the bot is activated, it will listen on a port located locally on your system. 27911 for an example. Some 'leet' cheats will even auto-copy it to your clipboard.
-You fire up your Quake2 client and use a command like 'connect localhost:27911'
-At this point the bot program recognizes the connection attempt and initiates a connect to your server of choice. The bot is acting as the middle-man in your connection to the server and does neat stuff by auto-adjusting your view so it acts like an aimbot.
The idea behind the protection is that the middle-man will pass on the reconnect command to your actual Q2 client. If you reconnect within your Q2 client, you'll reconnect to the localhost:27911 server and you'll either be stuck in an endless loop, or the protection will detect that you're not reconnecting properly and ban you.
Probably 5 years or more ago these bots have been hacked/patched by clever programs to evade this method of prevention/detection. I don't even know why VQ2 servers still use this, as it's pretty useless. PB2 which doesn't have an -- apparent -- aimbot problem and I wouldn't see the necessary to use this protection. Because like jitspoe mentioned, it would just only be a nuisance.