"IFrame"  is an HTML construct... and so - why "..don't want the script to be viewed..." ?? This could be done using jQuery/AJAX/PHP.. to wrest control of the actual JS/ HTML away from the browser. However if you want to "hide" the JS - no chance of stopping someone who knows jQ, JS,PHP - They'll get the code if they want ;-)

Now it stopped working when I added a new feature. The added new feature was a meebo chatroom.

ugh http://allinoneportal.com I was thinking about upgrading to elgg 1.7.4 but dunno if this will resolve this issue. Should I upgrade....lol 

The problem is likely a conflict between whatever you did to get links going to an iframe and the chatroom plugin. Upgrading is not going to fix that.