AFAIK there's no way to get rid of the upgrade popup.

Try deleting LW's preferences folder when LW's properly closed...see if that allows you to at least close the box again
See point 3 below for instructions. If you've used much older versions of LW, there could be a folder in point 2's location as well.
Fixes for LimeWire

*Deleting that folder will kill all of your settings within options. You'll have to go back through & reset things afterwards.

If that doesn't help, try installing the latest LW 4.12.11.
http://www.limewire.com/english/content/download.shtml
If you love your 4.9 version, make sure the installer is saved...installing a newer version of LW will automatically remove the previous version.