Howdy Nicholas!
That should be possible. I am sorry this is giving you a hassle. We actually are going to remove that JS soon and just use proper permalinks as your currently are.
In the mean time you could simply rename the css class applied to that element. If you create a theme override for pthe-events-calendar/src/views/list/nav.php, and replace these two lines with a different CSS class of your choosing it should disable any JS that applies to those links:
24:<li class="<?php echo esc_attr( tribe_left_navigation_classes() ); ?>">
31:<li class="<?php echo esc_attr( tribe_right_navigation_classes() ); ?>">
You have probably read this already, but you can easily override that template by following our Themer’s Guide.
Does that all make sense? Will that work for you?
Cheers!
– Brook