This will force the owners of H264 to either create a fair price for the codec in 2016, or they will become irrelevant like RealPlayer, etc.
Theora is a generation older than H.264. There are features in H.264 that help compression that aren't in Theora, plus Theora has a few other problems (e.g. motion vectors no longer than 16 pixels). So a good H.264 encoder is always going to beat a good Theora encoder. Perhaps they'll be able to create a truly excellent Theora encoder that will mitigate the format's deficiencies as much as possible, and outperform the majority of H.264 encoders, but I wouldn't bet on it. The open-source x264 encoder is already very good, and is only going to get better. And the increasing use of H.264 for TV broadcast and Blu-ray surely means that there's going to be strong competition amongst the vendors of commercial H.264 encoders.
...that said, I think you are right.