So...what do I do, then? Take the scientist elsewhere and go bumming around for a while before starting work on the anomaly? Or is it doomed to fail no matter what at this point?
Just let it fail. =| It's not such a big deal.
You're gonna fail some anomalies anyway and really they don't do THAT much. Unless you're only planning to ever play this once, you'll probably run into this anomaly again in the future. There really aren't so many that you'll never see this again.
Might as well. I decided to let the scientist in question go work on a different event, one requiring a 5-star scientist.
95% of the way through the project, an election was held and that same scientist became the President, leaving the science vessel stuck in place. And since she's a substance abuser in her late 50s, she's unlikely to survive long enough to get back to work.
I hate you so much, Stellaris.
* Sirus plays more Stellaris
Fun fact: if a construction ship abandons its task partway through (a threat appearing in the system, ferex), the partially-constructed station instantly disappears and all minerals spent on that project are lost. So that's nice.