I want to show a lock screen icon with counter as described here: http://msdn.microsoft.com/en-us/library/windowsphone/develop/jj207048(v=vs.105).aspx
However, when doing this, the counter is also shown on the main tile of the app. Can I avoid that? (counter on the tile looks really ugly).
You can't.
The lock screen icon is designed to be used with the iconic tile template, which will show the count.
The best you can do is to design the icon to work with the count.
If you don't like the count in principle then remember that you're not a typical user. The count and iconic tile template is used by lots of native apps and users of the phone will be familiar with it as they'll see it with lots of apps.
