Did you want the content viewable or not? If you don't want the content behind it visible, then you could add an additional CSS rule for background-color to the overlying div. Here's one for straight up white:
$('#content-wrapper').append('<div style="position:fixed;bottom:0;background-color:#fff;"><a href="http://www.example.com/link1">Link 1</a> <a href="http://www.example.com/link2">Link 2</a></div>');
If you did want it visible beneath somewhat you can adjust the transparent nature of the footer itself.
Here's another straight up white with some opacity built in using the CSS rgba color specification. The last number is one you can play around with. It's a floating decimal number between 0 and 1, with 1 being fully opaque and 0 being fully transparent:
$('#content-wrapper').append('<div style="position:fixed;bottom:0;background-color:rgba(255,255,255, 0.3);"><a href="http://www.example.com/link1">Link 1</a> <a href="http://www.example.com/link2">Link 2</a></div>');
Note that the div itself is only as wide as the content between the div tags. If you need it to cover the entire horizontal span of the content you would need a width CSS property of 100%.
If you want to play around with other values for the background-color rule I would encourage you to visit this w3schools page.
This is just the starting recipe. Add salt to your specific taste/need.