It's actually amazing that they ran the show at all given how much rain we had in the area last night.
But if they did, it would definitely have been a modified show, there were probably several other changes as well that you may or may not have noticed, depending on what they could get dried off in time.
And they usually do the stunts when it isn't raining, this is one of the modifications that get made.
There were probably fewer characters on the Mark Twain, especially on the upper deck. Depending on how much rain there is, they may not do the fireworks on the Mark Twain, as it isn't safe to have people that are not strapped in on the top deck and the Chimney Sweeps are there to make sure the boat doesn't catch on fire again. Sometimes they will abandon the Mark Twain completely in the rain and use the island, like they do when the Mark Twain is down for rehab. There will usually be fewer characters on the island when this happens due to rain, as some portions get quite slippery in the rain. There are even times when the princes/princesses and Monkeys fail to even make an appearance due to rain or may not be dancing around the stage. The dragon will usually not show up in the rain, as they have enough problems with her normally. Mickey will usually stay low on the island or will only show up for defeating the dragon (either real or the water replacement) and at the very end, but will not go up to the really high point. You may also find that the evil queen doesn't go through her transformation.
The show can also be shortened due to rain and/or cancelled midway through.
Can you tell that I have seen the show a few times? LOL
So if all that happened was the lack of stunts in the Peter Pan scene, you did indeed luck out.