Better to have a hungry BP than not.
I wouldn't remove her water bowl. I try not to mess with BP before feeding. They can get shy. Also, she might be in food mode for a while, but shouldn't be without her bowl for drinking or humidity, IMO.
This was probably a freak thing and I would work on getting the rat in faster. Also, I dry my rats before offering. I do use warm water to warm up the prey to get the pythons interested, but dry it before offering.
Shayna, BP, when ready, will nail her rat, but usually I end up putting down warmed up next to her hide and she comes out and nails it when I leave.
As Bogertophis alluded too, my Boas aren't as shy. I use the door to their PVC enclosure as a shield or go to the door they aren't at (my 6X2' Boaphiles have 2 acrylic doors). I also sometimes use the hook to open the door in case they strike out. However, I have them read pretty well at this point and luckily haven't had any food bites.
Some people get nervous about the strike but I find it's better to get the rat in front of them quick with the tongs - especially with boas and carpet python. They want the food and they want it NOW! They will strike wildly if not offered quickly and right in front of them - I don't knock them with it or anything - not the BP for sure, but the Boas I get it real close so they don't miss.