Transforming system link into a button
I definitely don't recommend hacking the module - it's not good Drupal form, and it limits your ability to get module updates in the future.

I think the answer depends on how the module creates the link in question. That is, how is the link HTML being generated? If it's being generated and printed directly to the screen, then you'd have to do some CSS/JS work to intercept the HTML being generated and alter it. We have done this when necessary on our site to bend certain modules and functionality to suit our display needs. If the link has a specific ID, just alter it with JS in a custom module or custom theme. If not, you may have to get at it via jQuery based on what elements it's contained within, but it can be done.

If you're lucky and the module is well-written, the link will be part of content that's passed through Drupal's theming engine first through a theme() call. In this case, you can write your own function to grab anything being themed, inspect it for whatever markers indicate that it should become a button, and then alter the link code as need be. If you're not familiar with the theme() functionality in Drupal, you'll want to read up on it on Drupal.org first. Hope this helps!