The MSDN documentation on WebBrowser Customization explains how to prevent new windows from being opened and how to cancel navigation. In my case, my application is hosting
I'm hypothesising here but yet another approach could be to maintain a count of navigation events, incrementing the counter on DISPID_BEFORENAVIGATE2 and decrementing it on occurrences of DISPID_NAVIGATECOMPLETE2 and DISPID_NAVIGATEERROR. With that in place, you could speculate that whenever you get DISPID_BEFORENAVIGATE2 and your counter is at zero, it is actual user navigation / link invocation.
I have no idea whether this approach would work, or whether those are the right events you'd need to make it work, but it could be worth investigating.