Note that none of what Johnson writes contradicts that the Crusades were in essence a just war. What Johnson does is, he spreads some key words to which a modern reader has a Pavlovian negative reaction, such as "indulgences" or "violence", or "mob of armed and fanatical Christians". He also silently takes for granted that the East was Muslim. I never thought of Johnson as a yellow historian before (I read his History of the American People and some polemical articles) but these quotes convince me otherwise.
These are mere excerpts from a much broader context. They fit well in his overall thesis. Rejecting him out-of-hand, as you do, ignores that.