Wow, I have 80+ hours of Commander under my belt (as witnessed by my ribbons) and I didn't knew THIS...
It's really horrible by the way - although the usefulness of this trick is lessened by the fact that the silos close to one's titan are already easily conquereable.
Now I understand why the battles to silo 4 were so furious... and if I knew this, I could have spared myself so many useless deaths at silo 5...
Well, for the future I will refrain from using this trick, unless the enemy commander does as well.
Anyone has ever studied under which conditions a silos' missiles which you control hit your own titan?