This plugin will allow you to disable plugin upgrade options for selected plugins.
Download the plugin, extract and upload it to your plugins folder on your server.
Activate the plugin.
Go to Plugins.
Click the link "Ignore Upgrade Option" next to the upgrade nag below a plugin.
Go to Settings->Ignore Plugin Upgrades to manage which plugins upgrades you are ignoring.
NOTE: If you are having issues with this plugin, please go to the plugin page and post a comment. If I don't know about it, I can't fix it.