They can still troll non-OSI-licensed projects with those patents and can still troll open source projects with new invalid patents.
We could stop issuing invalid patents (I'm not holding my breath), develop a legal defense fund to do this again (thus maybe scaring off future trolls) as the article suggests, or change the law.
If we change the law we could do something minimal like the article suggests (eg: allow proof the code being sued over predates the patent to be presented at the summary judgment stage) OR (my favorite) something bigger like eliminating software patents entirely.