Is there a way to remove a menu item from the active trail without removing it from the menu parent? I'm a relative newcomer to Drupal and I'm not sure how to handle this. On this page:

http://staging.stvincentdepaul.net/volunteer

You can see that Volunteer is highlighted in the main nav but so is Today. If you hover over those L1 links, you'll see that each one has a Donate and Volunteer button. These are all part of the main navigation menu in the admin section so each Donate and Volunteer button falls under each L1 link. The Today section was the last to have Donate/Volunteer added so it is attaching the active-trail class to that link since it can only have one.

Is there a way to keep those Donate/Volunteer links in the menu but not part of the active trail?
This is a common headache. I keep meaning to write a contrib module to address this by letting users define a "canonical" menu item in the event there are several menu items that point to the same page in the same menu.

That said, there are some workarounds you can use.

The best option is to use the Redirect module. You create a redirect to your Donate and Volunteer pages then put the redirects in the menus.

So if your volunteer page is at /volunteer and donate is at /donate, then you can create two redirects. One called /go-volunteer and another called /go-donate which redirect to their respective pages. Then you'd put /go-volunteer and /go-donate in the menu which, when clicked, will take the user to the appropriate page.

Since they're redirects, they won't trigger the active trail.