Ugh... sorry you have had this happen. That bacteria is hard to get rid of too. I'd say your best bet is to scoop them out, rinse the the agar off as best as you can, and soak them in peroxide for a couple minutes.
Yes, hydrogen peroxide is probably your best choice. Unfortunately, the concentration and time needed to kill the bacteria is likely to damage the protocorms too. You might want to try several small batches at different strengths or durations to have a better chance to save at least some of them.