Between Day 4 and Day 5, the leader of the Voodoo cult changed the message on the Laveau crypt to "DJ, keep eyes on GK but do not harm."

Yet on Day 5, when Gabriel visits the Voodoo Museum, Dr. John sics the snake on him. And I'm pretty sure that siccing a snake on someone counts as "harming" them.

So why did Dr. John disobey those orders?

I never thought Dr. John intentionally disobeyed the orders, but maybe he didn't mind if the snake actually killed Gabriel. Since Dr. John left the museum door unlocked, it could have been intended as a warning or a trap if he expected Gabriel to show up. In the novel Dr. John makes more of an effort to ask if Gabriel is okay and explain that it's not wise to enter dark places (IIRC). It's a tense scene with underlying implications, but overall I don't think Dr. John wanted to kill Gabriel (yet). Room for different interpretations, though.

I think the word "directly," while it's unsaid, is implied here. In other words, "Do not harm" means "Do not directly harm." Tetelo didn't want Dr. John to DIRECTLY kill Gabriel. She said nothing about harming Gabriel indirectly. So the trap at the museum was set up so Dr. John could get Gabriel killed without disobeying Tetelo's order.